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 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 4,154,666 A→G I23V (ATT→GTT)  yhfA → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,154,6660AG96.5% 198.1 / ‑1.8 58I23V (ATT→GTT) yhfAconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base G (30/26);  total (30/28)
Fisher's exact test for biased strand distribution p-value = 2.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

CAAGCGCGAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGGCGGCG  >  W3110S.gb/4154603‑4154731
                                                               |                                                                 
cAAGCGCGAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTaa                                                             <  1:1276413/70‑1 (MQ=255)
cAAGCGCGAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTaa                                                             <  1:2715080/70‑1 (MQ=255)
 aaGCGCGAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATg                                                           <  1:139546/71‑1 (MQ=255)
                gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAgg                                             >  1:2522612/1‑70 (MQ=255)
                gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                            >  1:927262/1‑71 (MQ=255)
                gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                            >  1:382717/1‑71 (MQ=255)
                 ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTa                                                              >  1:3388780/1‑52 (MQ=255)
                       aGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:47374/1‑71 (MQ=255)
                       aGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:3563717/1‑71 (MQ=255)
                       aGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:2933593/1‑71 (MQ=255)
                       aGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:1739067/1‑71 (MQ=255)
                       aGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTAAGGCGATAAAg                                     >  1:524716/1‑71 (MQ=255)
                        gggTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:1125072/1‑70 (MQ=255)
                        gggTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:676461/1‑70 (MQ=255)
                        gggTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:3403807/1‑70 (MQ=255)
                        gggTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:3132981/1‑70 (MQ=255)
                        gggTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAg                                     >  1:1396772/1‑70 (MQ=255)
                           ttAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTc                                                >  1:773423/1‑56 (MQ=255)
                           ttAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCg                                           >  1:1508991/1‑61 (MQ=255)
                           ttAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCAc                                  >  1:2222323/1‑70 (MQ=255)
                             aaCTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCAcc                                 >  1:745917/1‑69 (MQ=255)
                                  ttCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTcc                           <  1:177629/70‑1 (MQ=255)
                                  ttCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTcc                           <  1:293097/70‑1 (MQ=255)
                                                     tGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGAt         <  1:1304830/69‑1 (MQ=255)
                                                     tGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGAt         <  1:3303307/69‑1 (MQ=255)
                                                     tGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGAt         <  1:1417397/69‑1 (MQ=255)
                                                     tGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGAt         <  1:2862733/69‑1 (MQ=255)
                                                     tGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGAt         <  1:1971987/69‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt            <  1:639446/61‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt            <  1:3704004/61‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt            <  1:1524182/61‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGgcggcg  <  1:3495933/71‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGgcggcg  <  1:4131676/71‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGgcggcg  <  1:665709/71‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGgcggcg  <  1:1846673/71‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGgcggcg  <  1:1082842/71‑1 (MQ=255)
                                                          atcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGgcggcg  >  1:987772/1‑71 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATgg                <  1:3185853/56‑1 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATgg                <  1:191456/56‑1 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATgg                <  1:2634234/56‑1 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATgg                <  1:1323736/56‑1 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATgg                <  1:2957627/56‑1 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATgg                <  1:1620700/56‑1 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATgg                <  1:3208246/56‑1 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGgcggcg  <  1:274516/70‑1 (MQ=255)
                                                           tcaGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGgcggcg  <  1:814333/70‑1 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATgg                <  1:540740/55‑1 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:3786501/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:4112369/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:1651760/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:3739105/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:490927/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:1708786/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:2690704/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:1165962/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:2259105/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:19672/1‑61 (MQ=255)
                                                            caGGTTTTAATGGACGGCAACGCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGa          >  1:541555/1‑61 (MQ=255)
                                                               |                                                                 
CAAGCGCGAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGGCGGCG  >  W3110S.gb/4154603‑4154731

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A