Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F104 I1 R1	35	102.1	2392160	96.4%	2306042	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,063,805	+T	coding (684/1218 nt)	ywtF ←	Putative transcriptional regulator YwtF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,063,804	1	.	T	95.3%	419.1 / 12.8	128	coding (685/1218 nt)	ywtF	Putative transcriptional regulator YwtF
Reads supporting (aligned to +/- strand): ref base . (3/3); new base T (56/66); total (59/69)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

Only 100 of 131 total aligned reads displayed.

AATTTCAACATCATTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑A‑TAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTATC  >  USA300TCH1516_ALE/1063664‑1063939

aaTTTCAACATCATTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGa‑a                                                                                                                                          <  1:996582/141‑1 (MQ=255)

 aTTTCAACATCATTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑A‑t                                                                                                                                        <  1:960614/141‑1 (MQ=255)

  tttCAACATCATTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑A‑tt                                                                                                                                       <  2:383467/141‑2 (MQ=255)

        catcatTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATc                                                                                                                                  <  2:1007955/141‑1 (MQ=255)

               tGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCttaatta                                                                                                                           >  1:472832/1‑141 (MQ=255)

               tGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCttaatta                                                                                                                           >  1:953395/1‑141 (MQ=255)

               tGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATAACGTTATCAAGTTTCTCAATAGAATAAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCttattta                                                                                                                           >  2:1004112/1‑141 (MQ=255)

                tttAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCCACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCttaattaa                                                                                                                          <  1:827094/140‑1 (MQ=255)

                gTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATATAATCAACGTCC‑AGTGC‑TTTT‑TGGA‑ATTAAAATCttaattaa                                                                                                                          >  1:219528/1‑141 (MQ=255)

                      tACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCAt                                                                                                                    >  1:959561/1‑141 (MQ=255)

                        cATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCAttt                                                                                                                  >  2:478594/1‑141 (MQ=255)

                              tGCTAAAGCTTTAACTTCAGAGTTAATTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGtt                                                                                                            >  1:657593/1‑141 (MQ=255)

                              tGCTAAAGATTTAATTTCAGAGTTAGTTAAATTATGCTTTGCCTTTTTACATACAATTTGAATCACGTTATCAAGTTTATCAATAGGATCAACTTCC‑TGTGC‑TTTT‑TGGACT‑TAAAATCTTAATTAATTCCCTTTGTCGtt                                                                                                            >  2:879461/1‑141 (MQ=255)

                               tcTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTGATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTg                                                                                                           <  2:104627/140‑1 (MQ=255)

                               gCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTg                                                                                                           >  1:273418/1‑141 (MQ=255)

                                       tttAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGtt                                                                                                   >  1:764295/1‑141 (MQ=255)

                                         tAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTCACTACAATTTGTATCACGTTATCAAGTTTAAAAATTTGATCAACTAAC‑AATTG‑TGTT‑TTGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGtttt                                                                                                 <  1:1176476/141‑1 (MQ=255)

                                          aaTTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGGTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGTCGTTGTCCACGTTTTa                                                                                                <  1:974000/141‑1 (MQ=255)

                                           aattCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTaa                                                                                               <  1:682153/139‑1 (MQ=255)

                                            tttCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TTGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTCAg                                                                                              >  1:351112/1‑141 (MQ=255)

                                             ttCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACTTTGTCCATGTTTTAGGt                                                                                             >  1:306609/1‑141 (MQ=255)

                                               cAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTTCACGTTTTAAGttg                                                                                           >  1:1106325/1‑139 (MQ=255)

                                               cAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCt                                                                                           <  2:680417/141‑1 (MQ=255)

                                               cAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCt                                                                                           <  2:952036/141‑1 (MQ=255)

                                                agagTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTg                                                                                          >  1:841889/1‑141 (MQ=255)

                                                 gagTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGa                                                                                         >  1:1035605/1‑141 (MQ=255)

                                                   gttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAATTCTGAAt                                                                                       <  1:746738/141‑1 (MQ=255)

                                                   gttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAAt                                                                                       <  2:292389/141‑1 (MQ=255)

                                                    ttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCAGGTTTTAAGTCTGAATc                                                                                      >  1:153430/1‑141 (MQ=255)

                                                    ttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTACGTCTGAAta                                                                                      >  2:249092/1‑140 (MQ=255)

                                                    ttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTTTGAAta                                                                                      >  2:738024/1‑140 (MQ=255)

                                                    ttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATc                                                                                      >  1:410080/1‑141 (MQ=255)

                                                    ttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATc                                                                                      >  1:988107/1‑141 (MQ=255)

                                                     tagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCa                                                                                     <  2:505409/141‑1 (MQ=255)

                                                          aaaTTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCatgatg                                                                                <  2:192333/141‑1 (MQ=255)

                                                           tatgaTGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATTAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGt                                                                               <  2:814964/137‑1 (MQ=255)

                                                             ttATGCTTTACAATTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCt                                                                             <  2:419680/141‑1 (MQ=255)

                                                                   tttGCATTTTTACCTACACTTTGTAACACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCt                                                                       <  2:834017/141‑1 (MQ=255)

                                                                   tttGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCt                                                                       <  1:471501/141‑1 (MQ=255)

                                                                   tttGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCt                                                                       <  2:272601/141‑1 (MQ=255)

                                                                   tttGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCt                                                                       <  2:9446/141‑1 (MQ=255)

                                                                   tttGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCt                                                                       >  1:673207/1‑141 (MQ=255)

                                                                   tttGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTG‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCt                                                                       <  1:1099060/141‑1 (MQ=255)

                                                                   tttGCATTTTGACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGACTCAACTCCC‑TGTGC‑TGTC‑TGGACT‑TCAATTCTTAATTAATTACATTTCACGTTGGTCACGTTTTAAGTCTCAATTATGATGTCTAGTTCt                                                                       <  1:891886/141‑1 (MQ=255)

                                                                   tgtGCATTTTTACCTAGCATTTGAATCACTTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAATATCTTTATTAATTCCATTTGACGTTGTCTACGTTTGATGTCTGAATCATGATGTCTAGTTCt                                                                       <  2:388235/139‑1 (MQ=255)

                                                                    ttGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTa                                                                      <  2:57240/141‑1 (MQ=255)

                                                                    ttGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTa                                                                      <  2:920464/141‑1 (MQ=255)

                                                                       cATTTTTTCCTACAATTTGCATCACGTTATCAAGTTTATCAATACAATCGACTTCC‑TGTTC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCa                                                                   <  2:478576/141‑1 (MQ=255)

                                                                        aTTTTTAGCGACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCaa                                                                  <  2:947145/141‑1 (MQ=255)

                                                                         tttttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAAc                                                                 <  2:450880/141‑1 (MQ=255)

                                                                         tttttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAAc                                                                 <  2:889542/141‑1 (MQ=255)

                                                                         tttttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAAc                                                                 >  1:697110/1‑141 (MQ=255)

                                                                          ttttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACt                                                                <  1:830297/141‑1 (MQ=255)

                                                                           tttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTATCAACTg                                                               <  2:660900/141‑1 (MQ=255)

                                                                           tttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTg                                                               <  2:855946/141‑1 (MQ=255)

                                                                            ttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGc                                                              <  1:1020793/141‑1 (MQ=255)

                                                                              aCCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTa                                                            >  1:494255/1‑141 (MQ=255)

                                                                               ccTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTaa                                                           >  2:105043/1‑141 (MQ=255)

                                                                                  aCAAGTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGc                                                        <  1:228598/141‑1 (MQ=255)

                                                                                   cAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGcc                                                       <  1:890611/141‑1 (MQ=255)

                                                                                   aaaTTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGcc                                                       <  1:697025/140‑1 (MQ=255)

                                                                                        tGAATCACGTTATCAAGTTTCTAGTTACGGACAGCTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTGGTTCTAGCAACTGCTAAAGCCtcatc                                                  >  1:878161/1‑141 (MQ=255)

                                                                                        tGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCtcatc                                                  >  1:1174373/1‑141 (MQ=255)

                                                                                        tGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCtaatc                                                  >  1:700717/1‑141 (MQ=255)

                                                                                        tGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑AGTGC‑GTGT‑TGGA‑ATTAAAATCTTACTTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCtcatc                                                  >  1:526234/1‑141 (MQ=255)

                                                                                         gAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTATAGCCtcatca                                                 <  2:807504/141‑1 (MQ=255)

                                                                                          aaTCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGCTTTTT‑TTTT‑T‑TTTTTTTTTAATTAATTCCCTTTGACGTTATCCACGTTTTAATTTTGAATCATGATGTCTGCTTCTAGCACTTCCTAACTCTTCATCAc                                                >  2:1157314/1‑141 (MQ=255)

                                                                                          aaTCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCAc                                                >  1:458125/1‑141 (MQ=255)

                                                                                          aaTCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCAc                                                >  2:307704/1‑141 (MQ=255)

                                                                                          aaTCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCAc                                                >  1:227249/1‑141 (MQ=255)

                                                                                          aaTCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCATCATAAc                                                >  1:637267/1‑141 (MQ=255)

                                                                                          aaTCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCCAAAGCCTCATCAc                                                >  2:1157409/1‑141 (MQ=255)

                                                                                           aTCACGTTATCAAGTTTATCAATAGAATCAACTTCA‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGCATCATGATGTCTAGTTCTAGCAACTGCTCAAGACTCATCAca                                               >  2:392848/1‑140 (MQ=255)

                                                                                             cACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTTTCCACGTTTTAAGTCTGAATTATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCAt                                             <  1:1003191/141‑1 (MQ=255)

                                                                                                gTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTTGTGAA‑T‑TAAAATCTTCATTAATTCCATTTGACGTTGTCCACGTTTGAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCCTTTa                                          >  2:474316/1‑141 (MQ=255)

                                                                                                gTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTCTAAGTCTGAATCATGATGTCTAGTTCTGGCAACTGCTAAAGCCTCATCACCATTTa                                          >  1:413565/1‑141 (MQ=255)

                                                                                                   aTCAAGTTTATCAATAGAATCAACCTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAAtt                                       <  1:323554/141‑1 (MQ=255)

                                                                                                    tCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTTATCACTTAGTTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAAttt                                      <  1:863465/141‑1 (MQ=255)

                                                                                                    tCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTCATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAAttt                                      <  1:215552/141‑1 (MQ=255)

                                                                                                    tCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAAttt                                      <  1:1195540/141‑1 (MQ=255)

                                                                                                     cAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAAtttt                                     >  1:154963/1‑141 (MQ=255)

                                                                                                     cAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTGT‑TGGA‑ATTAAAATCTTAATGACTTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAATCCTCATCACCATTTAAtttt                                     <  2:655670/141‑1 (MQ=255)

                                                                                                                aTAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCttt                          >  2:41500/1‑141 (MQ=255)

                                                                                                                   gAATCATCTTCCTTGTCT‑TTTT‑TGAA‑T‑TAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCtttttt                       <  2:230709/141‑1 (MQ=255)

                                                                                                                      tCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAAGTGCTAAAGCCTCATCACCATTTAATTTTTGGTAGCCTTttttaat                    >  2:641054/1‑141 (MQ=255)

                                                                                                                      tCAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACCTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTGTGGTACCCTTttttaat                    >  2:801570/1‑141 (MQ=255)

                                                                                                                       cAACTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAAACTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTttttaatt                   >  1:769911/1‑141 (MQ=255)

                                                                                                                         aCTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTttttaatttt                 >  1:118008/1‑141 (MQ=255)

                                                                                                                         aCTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTttttaatttt                 >  1:376895/1‑141 (MQ=255)

                                                                                                                         aCTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCAAATGTCTGTGGGTACCCTTttttaatttt                 <  1:579233/141‑1 (MQ=255)

                                                                                                                          cTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAGTCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCCTCACGATTGAATTTTTGGTCCCCTTttttaatttta                >  1:1015476/1‑141 (MQ=255)

                                                                                                                          cTTCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGTCGTTGTCCACGATTTAAGTCTGAATCATGATGTCTAGTTCTAGCACATGCTACAGCATCATCACCTTTTAATTTTTGGTACAATTttttcattttt                >  2:645017/1‑140 (MQ=255)

                                                                                                                           ttCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTtttaaattttaa               >  2:863407/1‑141 (MQ=255)

                                                                                                                            tCC‑TGTGC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTtttaattttaat              >  2:408614/1‑141 (MQ=255)

                                                                                                                                tgtgC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTCAAGCCTCATCACCATTTAATTTTTGGTACCATTTTTTAATTTTAATCtt           >  2:593026/1‑141 (MQ=255)

                                                                                                                                tgtgC‑TTTT‑TGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCtt           >  1:1132006/1‑141 (MQ=255)

                                                                                                                                       ttt‑tGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGt     <  1:400330/141‑1 (MQ=255)

                                                                                                                                         t‑tGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTat   <  1:269299/141‑1 (MQ=255)

                                                                                                                                           tGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTGAGTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTatc  <  2:494255/141‑1 (MQ=255)

                                                                                                                                           tGGA‑ATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTatc  <  2:1143090/141‑1 (MQ=255)

AATTTCAACATCATTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCC‑TGTGC‑TTTT‑TGGA‑A‑TAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTATC  >  USA300TCH1516_ALE/1063664‑1063939

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A