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
A23 F74 I0 R1	29	68.9	1565664	94.4%	1477986	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,049	A→G	54.2%	V199A (GTT→GCT)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,049	0	A	G	54.2%	8.2 / 68.5	59	V199A (GTT→GCT)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (16/11); new base G (12/20); total (28/31)
Fisher's exact test for biased strand distribution p-value = 1.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.60e-01

GCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATT  >  USA300TCH1516_ALE/2027913‑2028188

gCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCttt                                                                                                                                         >  1:278265/1‑141 (MQ=255)

   ttGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATTTTGTTATTTTAAACTTtata                                                                                                                                      >  1:519130/1‑141 (MQ=255)

     gAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATg                                                                                                                                    <  1:415160/141‑1 (MQ=255)

     gAACCAATCGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATg                                                                                                                                    <  1:415374/141‑1 (MQ=255)

       tccAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGAt                                                                                                                                  <  2:194584/140‑1 (MQ=255)

          aaTTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGAtttt                                                                                                                               >  1:126740/1‑141 (MQ=255)

           aTTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGAttttt                                                                                                                              >  2:184290/1‑141 (MQ=255)

             tGTTCTAATGTAGTGGTTCATCGATAAGTCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTttca                                                                                                                            <  2:242312/141‑1 (MQ=255)

              gTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCCACTTTATATGATTTttcat                                                                                                                           >  1:691671/1‑141 (MQ=255)

               ttCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTttcatt                                                                                                                          >  1:422899/1‑141 (MQ=255)

               ttCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCAACGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTttcatt                                                                                                                          <  2:734078/141‑1 (MQ=255)

                 cTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTttcagtcc                                                                                                                        >  1:731841/1‑140 (MQ=255)

                    aTGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGt                                                                                                                     <  1:750375/141‑1 (MQ=255)

                     tGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTa                                                                                                                    <  2:399347/141‑1 (MQ=255)

                     tGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACCGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTa                                                                                                                    <  2:95890/141‑1 (MQ=255)

                         gTGGTTCATCGATAAATCAGCTCTACGTCGCCGATACACTTTGATACGGAGATATTATCTGTATAGTTATCCGGTTTCATCATGTCTTTAATATGAATATTTTTATTTTCAGCTTTATATGGTTGTTCATTCACGTAAGTa                                                                                                                <  1:356626/141‑1 (MQ=255)

                           ggTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACt                                                                                                              >  2:29067/1‑141 (MQ=255)

                               cATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCa                                                                                                          <  2:631697/141‑1 (MQ=255)

                                 tCGATAAATCACCTCTACTTCTCCGATAAACGTTGATACGTAGATATTAACGGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCGTTATATGATTTTTCATTCACGTAAGTACTTCCATa                                                                                                        <  2:278324/141‑1 (MQ=255)

                                 tCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATa                                                                                                        <  2:569470/141‑1 (MQ=255)

                                 tCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATa                                                                                                        <  2:675415/141‑1 (MQ=255)

                                  cGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATTATTTTTCATTCACTTAAGTACTTCCAtca                                                                                                       >  2:400082/1‑139 (MQ=255)

                                  cGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATaa                                                                                                       >  2:71075/1‑141 (MQ=255)

                                        aTCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCCTAAAAagca                                                                                                 >  2:108056/1‑141 (MQ=255)

                                        aTCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAagca                                                                                                 <  1:644483/141‑1 (MQ=255)

                                         tCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCGCGTAAGTACTTCCATAAGAagcag                                                                                                >  1:587757/1‑141 (MQ=255)

                                          cACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAagcagc                                                                                               >  1:719093/1‑141 (MQ=255)

                                           aCCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCt                                                                                              <  2:611242/141‑1 (MQ=255)

                                               ctACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACAt                                                                                          <  2:743830/141‑1 (MQ=255)

                                                tACGTTTGCTATAAACGTTGATACGTAGATATTAACTGTATAGTTATGCGGTTTCATCATTTCTTCAATATTAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATg                                                                                         <  2:23556/141‑1 (MQ=255)

                                                 aCGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGt                                                                                        <  1:633412/141‑1 (MQ=255)

                                                  cGTCTCCGATAAACGTAGATACGTTGATATTAACTTTAGAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAGGCAGCTACATGTa                                                                                       >  1:188911/1‑141 (MQ=255)

                                                   gTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTaa                                                                                      <  1:678782/141‑1 (MQ=255)

                                                      tcCGATAAACTGTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAAtt                                                                                   <  1:565774/141‑1 (MQ=255)

                                                            aaaCGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTAATGTAGGTACGTCCATAAAAAGCAGCTACATGTAAATTAATAtt                                                                             >  1:532006/1‑141 (MQ=255)

                                                              aCGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATAGTTAGTTGCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAACATCAGCTACATTTAAATTAATAtttt                                                                           >  2:634588/1‑139 (MQ=255)

                                                                tttGATACGGAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTaa                                                                         <  2:442537/140‑1 (MQ=255)

                                                                              atTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAatat                                                           <  1:327795/141‑1 (MQ=255)

                                                                              atTAACTGTATAGTTATCCGGTTTCATCATTTCTTAAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTAATTCCATAAAAAGCAGCTACATTTAAATTAATATTGTAATTAACAGGCAatat                                                           >  2:104241/1‑141 (MQ=255)

                                                                                tAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATaa                                                         <  1:118095/141‑1 (MQ=255)

                                                                                 aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTTTTTTTTTTTATTACTTCCATAAAAAGCAACTACATGTAAATTAATATTGTAATTAACCGGCActatctc                                                        >  2:442192/1‑138 (MQ=255)

                                                                                  aCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTATATTAATATTGTAGTTAACCGGCCATATAAcc                                                       >  1:88856/1‑141 (MQ=255)

                                                                                  aCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAAcc                                                       >  1:93034/1‑141 (MQ=255)

                                                                                    tGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAACTTAATATTGTAATTAACCAGCAATATAACCTg                                                     >  2:496296/1‑141 (MQ=255)

                                                                                      tataGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATATAAATTAATATTCTAATTAACCGACAATACAAcataca                                                   >  2:17672/1‑136 (MQ=255)

                                                                                               ccGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTa                                          >  2:601512/1‑141 (MQ=255)

                                                                                               ccGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACAGAAAAAACAACCTGCACTTTACCTa                                          <  2:285363/141‑1 (MQ=255)

                                                                                                   tttCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAACATAATCTCCACTTTACATAAAAt                                      >  2:712636/1‑141 (MQ=255)

                                                                                                   tttCATCATTTCTTCAATATGAATATTGTTATTGTCAGCCTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAAt                                      <  1:108056/141‑1 (MQ=255)

                                                                                                      catcatTTCTTCAATATGAATATTGTTATCTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAAtgtg                                   <  2:584785/141‑1 (MQ=255)

                                                                                                         catTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCt                                <  1:436534/141‑1 (MQ=255)

                                                                                                             tcttcAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTaaca                            <  2:496782/141‑1 (MQ=255)

                                                                                                                tcAATAGGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTAATTCCATAAAAAGCAGCTACATGTAAATTACTTTTGTAATTAACCGTCAATATAACATGCACTTTACTTAAACTGTGTCTacacaca                         >  2:598972/1‑135 (MQ=255)

                                                                                                                 cAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTATAATTAACAGACAATATAACCTACACTTTACCTAAAATGTGTCTAAcaacaa                        >  2:369684/1‑141 (MQ=255)

                                                                                                                     atGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGt                    <  2:409677/141‑1 (MQ=255)

                                                                                                                                 aTTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCtt        <  2:126740/141‑1 (MQ=255)

                                                                                                                                 aTTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAACAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCtt        >  2:502003/1‑141 (MQ=255)

                                                                                                                                  ttttCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTa       >  1:30979/1‑141 (MQ=255)

                                                                                                                                   tttCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTaa      <  1:471/141‑1 (MQ=255)

                                                                                                                                       aaCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATAtt  <  1:761696/141‑1 (MQ=255)

GCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATT  >  USA300TCH1516_ALE/2027913‑2028188

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