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
A5 F58 I0 R1	46	56.2	1222162	96.0%	1173275	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,539,250	C→G	100%	intergenic (‑349/+37)	aroC ← / ← USA300HOU_RS07505	Chorismate synthase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,539,250	0	C	G	84.4%	97.9 / 10.9	40	intergenic (‑349/+37)	aroC/USA300HOU_RS07505	Chorismate synthase/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/6); new base G (17/15); total (17/23)
Fisher's exact test for biased strand distribution p-value = 2.41e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAGTTGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGT  >  USA300TCH1516_ALE/1539112‑1539385

cAGTTGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCg                                                                                                                                       <  1:355970/141‑1 (MQ=255)

  gTTGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGtt                                                                                                                                     <  1:236901/141‑1 (MQ=255)

     gCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATAAGTGCGTTTaa                                                                                                                                  >  2:422956/1‑141 (MQ=255)

               aTCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTAtt                                                                                                                        >  2:388438/1‑140 (MQ=255)

                     aattaaAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTa                                                                                                                  <  1:564326/141‑1 (MQ=255)

                        taaAAATTATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACTAACTGTTAATTATTAATAAAGTTAATTAGTCCGTTTAAAAAAATTATGATATTaaaa                                                                                                               <  2:491393/141‑1 (MQ=255)

                        taaAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTaaaa                                                                                                               <  1:591462/141‑1 (MQ=255)

                            aaTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAATGCGTTTACAAAAATTATGATATTAAAAaata                                                                                                           >  2:298803/1‑141 (MQ=255)

                             aTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATGCGTTCATTTAAAAAAATTATGATATTAAAATATAc                                                                                                          <  1:296504/141‑1 (MQ=255)

                             aTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATAc                                                                                                          <  2:342680/141‑1 (MQ=255)

                             aTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATAc                                                                                                          <  1:285074/141‑1 (MQ=255)

                             aTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATAc                                                                                                          <  1:186675/141‑1 (MQ=255)

                             aTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTACGGCTAAAAAAATTATGATATTAAAATATAc                                                                                                          <  1:296456/141‑1 (MQ=255)

                               gATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACat                                                                                                        <  2:302120/141‑1 (MQ=255)

                                          ttAATAAAATCGTATCGCAACGTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAgcgc                                                                                             <  2:253456/141‑1 (MQ=255)

                                                   tCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTtat                                                                                    >  1:548237/1‑141 (MQ=255)

                                                      tATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACt                                                                                 >  1:186385/1‑141 (MQ=255)

                                                             aCTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACtt                                                                          <  1:131819/141‑1 (MQ=255)

                                                                        taataTACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATaa                                                               >  2:574308/1‑141 (MQ=255)

                                                                            ttaCTGACTACATTTCTTAATACAAAAGAACGAACTGTTTATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACGGATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCaa                                                           <  1:237697/140‑1 (MQ=255)

                                                                            ataCTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCaa                                                           <  1:469739/141‑1 (MQ=255)

                                                                             taCTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAAt                                                          >  2:189588/1‑141 (MQ=255)

                                                                                 gACTACATTTCATAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTAGACTTCAAAAATATAATCAATTCtt                                                      <  2:54803/141‑1 (MQ=255)

                                                                                          tCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATa                                             <  1:151633/141‑1 (MQ=255)

                                                                                           cTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATAc                                            <  1:330468/141‑1 (MQ=255)

                                                                                                     aaGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAata                                  <  1:532203/141‑1 (MQ=255)

                                                                                                     aaGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTGTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAata                                  >  1:583094/1‑141 (MQ=255)

                                                                                                         acgaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATaaa                              >  2:207361/1‑141 (MQ=255)

                                                                                                          cgaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACAGATGTTAAGCGCTTTTGTTATAAGTTGACTGTAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAAt                             >  2:430216/1‑141 (MQ=255)

                                                                                                           gaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATg                            >  1:150374/1‑141 (MQ=255)

                                                                                                                   aaTTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAg                    >  1:61333/1‑141 (MQ=255)

                                                                                                                      tattaATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTACAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCCGtaa                 >  2:99643/1‑140 (MQ=255)

                                                                                                                          aataaAGTTAAACAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATaaaa             <  2:340122/141‑1 (MQ=255)

                                                                                                                           ataaAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATaaaaa            <  1:569364/141‑1 (MQ=255)

                                                                                                                           ataaAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATaaaaa            <  1:478249/141‑1 (MQ=255)

                                                                                                                               aGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGACAGTATAAAaataat        >  1:41035/1‑141 (MQ=255)

                                                                                                                                  tAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAAtttt     >  2:318375/1‑141 (MQ=255)

                                                                                                                                  tAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAAttat     >  2:318529/1‑139 (MQ=255)

                                                                                                                                     tCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGt  >  2:423922/1‑141 (MQ=255)

                                                                                                                                     tCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGt  <  1:189588/141‑1 (MQ=255)

CAGTTGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGT  >  USA300TCH1516_ALE/1539112‑1539385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A