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 F8 I0 R2 422 46.8 3726540 94.7% 3529033 61.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,135,166 A→G 81.1% intergenic (‑139/+153) pitB ← / ← gss phosphate transporter/fused glutathionylspermidine amidase and glutathionylspermidine synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,135,1660AG81.1% 172.9 / 32.4 74intergenic (‑139/+153)pitB/gssphosphate transporter/fused glutathionylspermidine amidase and glutathionylspermidine synthetase
Reads supporting (aligned to +/- strand):  ref base A (12/2);  new base G (26/34);  total (38/36)
Fisher's exact test for biased strand distribution p-value = 6.32e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01

TGAAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGAATAAA  >  W3110S.gb/3135097‑3135232
                                                                     |                                                                  
tGAAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCaaaa                                                                   >  1:3388808/1‑71 (MQ=255)
tGAAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCaaaa                                                                   >  1:3107375/1‑71 (MQ=255)
tGAAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCaaaa                                                                   >  1:2533299/1‑71 (MQ=255)
tGAAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCaaaa                                                                   >  1:2038479/1‑71 (MQ=255)
tGAAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCaaaa                                                                   >  1:1353385/1‑71 (MQ=255)
tGAAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCaaaa                                                                   >  1:559650/1‑71 (MQ=255)
    atatCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCtt                                                               <  1:974848/71‑1 (MQ=255)
    atatCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCtt                                                               <  1:2287291/71‑1 (MQ=255)
    atatCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCtt                                                               <  1:617122/71‑1 (MQ=255)
    atatCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCtt                                                               >  1:3658994/1‑71 (MQ=255)
    atatCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCtt                                                               >  1:3052351/1‑71 (MQ=255)
    atatCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCtt                                                               >  1:2047232/1‑71 (MQ=255)
     tatCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCtt                                                               >  1:2944938/1‑70 (MQ=255)
     tatCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCtt                                                               >  1:1268797/1‑70 (MQ=255)
      atCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCtt                                                               >  1:441988/1‑69 (MQ=255)
       tCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCtt                                                               >  1:1849102/1‑68 (MQ=255)
         aTTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGAc                                                                  >  1:2498162/1‑63 (MQ=255)
         aTTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAg                                                            >  1:1733209/1‑69 (MQ=255)
         aTTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGa                                                           >  1:3590784/1‑70 (MQ=255)
            ttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAaat                                                        >  1:3452635/1‑70 (MQ=255)
            ttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAaat                                                        >  1:3027469/1‑70 (MQ=255)
                 aCGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCaa                                                  <  1:3218757/71‑1 (MQ=255)
                   gATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCaaaa                                                <  1:2767897/71‑1 (MQ=255)
                       aaaaGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAacac                                             <  1:1606950/70‑1 (MQ=255)
                             gtgtTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTAtt                                      >  1:1805605/1‑71 (MQ=255)
                                ttATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCaa                                                  <  1:485951/56‑1 (MQ=255)
                                ttATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCaa                                                  <  1:3092424/56‑1 (MQ=255)
                                ttATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCaa                                                  <  1:2463652/56‑1 (MQ=255)
                                ttATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTAt                                       <  1:840972/67‑1 (MQ=255)
                                ttATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTAt                                       <  1:680740/67‑1 (MQ=255)
                                ttATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTAt                                       <  1:387652/67‑1 (MQ=255)
                                  aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAg                                           >  1:1509269/1‑61 (MQ=255)
                                  aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCAc                                  >  1:3435503/1‑70 (MQ=255)
                                  aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCAc                                  >  1:1437795/1‑70 (MQ=255)
                                  aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACt                                 >  1:666877/1‑71 (MQ=255)
                                   tttCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        <  1:2417797/47‑1 (MQ=255)
                                   tttCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        <  1:2701830/47‑1 (MQ=255)
                                   tttCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        <  1:1635025/47‑1 (MQ=255)
                                   tttCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        <  1:532058/47‑1 (MQ=255)
                                     tCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCaaaa                                                >  1:1302461/1‑53 (MQ=255)
                                     tCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGt                              >  1:2335058/1‑71 (MQ=255)
                                     tCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGt                              >  1:963548/1‑71 (MQ=255)
                                     tCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTACACTGGt                              >  1:2895741/1‑71 (MQ=255)
                                      cTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTa                                                             >  1:407027/1‑39 (MQ=255)
                                          tgtATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAata                         <  1:1403289/71‑1 (MQ=255)
                                             aTCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCaa                                                  <  1:390327/43‑1 (MQ=255)
                                              tCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAatatat                      >  1:1504691/1‑70 (MQ=255)
                                              tCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAatatat                      >  1:1380340/1‑70 (MQ=255)
                                              tCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATAtt                     >  1:3393629/1‑71 (MQ=255)
                                                    aaTAAGCATTCATTCAAGACCTTTAGAAATACTCAAAACACAGGTATTCCACTGGtt                             <  1:2560959/57‑1 (MQ=255)
                                                    aaTAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGtt                             <  1:289825/57‑1 (MQ=255)
                                                    aaTAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGtt                             <  1:2501434/57‑1 (MQ=255)
                                                    aaTAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACata               >  1:1689813/1‑71 (MQ=255)
                                                     aTAAGCATTCATTCAAAACCTTTAGAAATAATCaaaa                                                <  1:3107001/37‑1 (MQ=255)
                                                     aTAAGCATTCATTCAAAACCTTTAGAAATAATCaaaa                                                <  1:1311014/37‑1 (MQ=255)
                                                       aaGCATTCATTCAAGACCTTTAGAAATAATCAAAac                                               >  1:1133270/1‑36 (MQ=255)
                                                        aGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAg                                           >  1:1413654/1‑39 (MQ=255)
                                                        aGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAg                                           >  1:1548917/1‑39 (MQ=255)
                                                        aGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAg                                           >  1:2273739/1‑39 (MQ=255)
                                                        aGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATatga            <  1:1360770/70‑1 (MQ=255)
                                                        aGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATatga            <  1:1665002/70‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTc                                     <  1:2554542/41‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTc                                     <  1:2751774/41‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTc                                     <  1:1523989/41‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTc                                     <  1:1380534/41‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:1256132/51‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:515144/51‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:3121643/51‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTcaca                 <  1:2629080/61‑1 (MQ=255)
                                                            ttcattcaAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTcaca                 <  1:2423564/61‑1 (MQ=255)
                                                              cattcaAGACCTTTAGAAATAATCAAAACACAGGTa                                        >  1:2712223/1‑36 (MQ=255)
                                                              cattcaAGACCTTTAGAAATAATCAAAACACAGGTa                                        >  1:1483599/1‑36 (MQ=255)
                                                              cattcaAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATatgaaatgaa      >  1:908897/1‑70 (MQ=255)
                                                                ttcaAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATatga            <  1:3559109/62‑1 (MQ=255)
                                                                ttcaAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATatga            <  1:3403410/62‑1 (MQ=255)
                                                                  caAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACata               >  1:1027444/1‑57 (MQ=255)
                                                                  caAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACata               >  1:3376397/1‑57 (MQ=255)
                                                                  caAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGaataaa  >  1:770544/1‑70 (MQ=255)
                                                                  caAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGaataaa  >  1:74525/1‑70 (MQ=255)
                                                                  caAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGaataaa  >  1:3648608/1‑70 (MQ=255)
                                                                     |                                                                  
TGAAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGAATAAA  >  W3110S.gb/3135097‑3135232

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A