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 F3 I0 R2 260 44.3 3360226 90.5% 3041004 64.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,135,166 A→G 49.3% 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.gb3,135,1660AG49.3% ‑5.5 / 111.1 76intergenic (‑139/+153)pitB/gssphosphate transporter/fused glutathionylspermidine amidase and glutathionylspermidine synthetase
Reads supporting (aligned to +/- strand):  ref base A (4/34);  new base G (24/13);  total (29/47)
Fisher's exact test for biased strand distribution p-value = 1.03e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.64e-01

AAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGAATAAA  >  W3110S.gb/3135099‑3135232
                                                                   |                                                                  
aaaTATCATTTTTTTACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:2515379/70‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAcc                                                                 <  1:2182000/71‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAcc                                                                 <  1:2315618/71‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAcc                                                                 <  1:2757137/71‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAcc                                                                 <  1:1178353/71‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAcc                                                                 <  1:558138/71‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:1676672/70‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:2707975/70‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:3206412/70‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:3283750/70‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:601354/70‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:1082166/70‑1 (MQ=255)
aaaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCAATCAAAAc                                                                  <  1:1550270/70‑1 (MQ=255)
 aaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:1044934/69‑1 (MQ=255)
 aaTATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAAc                                                                  <  1:756256/69‑1 (MQ=255)
         tttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGaa                                                          <  1:2948245/69‑1 (MQ=255)
         tttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGaa                                                          <  1:730061/69‑1 (MQ=255)
         tttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGaa                                                          <  1:1787793/69‑1 (MQ=255)
         tttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGaa                                                          <  1:1921329/69‑1 (MQ=255)
         tttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGaa                                                          <  1:2442945/69‑1 (MQ=255)
         tttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGaa                                                          <  1:406952/69‑1 (MQ=255)
          ttttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACATTTAGAaat                                                        >  1:1882078/1‑70 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:2721295/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:950131/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:2648123/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:790156/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:2504402/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:68751/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:1432162/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:1856827/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:1991326/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:1109501/1‑69 (MQ=255)
           tttAACGATAAAAAGAGTGTTATTTCTTGTGTAACAGACAATAAGCATTCATTCAAGACCTTTAGAaat                                                        >  1:2061453/1‑69 (MQ=255)
                 gATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCaaaa                                                <  1:304946/71‑1 (MQ=255)
                 gATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCaaaa                                                <  1:272980/71‑1 (MQ=255)
                 gATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATT‑‑AAACCTTTAGAAATAATCAAAaca                                              <  1:879409/71‑1 (MQ=255)
                   tAAAAATAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:126247/71‑1 (MQ=255)
                   tAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:2014861/71‑1 (MQ=255)
                   tAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:668775/71‑1 (MQ=255)
                   tAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:24386/71‑1 (MQ=255)
                   tAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:1713610/71‑1 (MQ=255)
                   tAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:868406/71‑1 (MQ=255)
                   tAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:3234979/71‑1 (MQ=255)
                   tAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:1686424/71‑1 (MQ=255)
                   tAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:3016100/71‑1 (MQ=255)
                   tAAAAAGACTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAaca                                              <  1:2642818/71‑1 (MQ=255)
                     aaaaGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAacac                                             <  1:2065798/70‑1 (MQ=255)
                                aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACt                                 >  1:542694/1‑71 (MQ=255)
                                aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACt                                 >  1:140232/1‑71 (MQ=255)
                                aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACt                                 >  1:333783/1‑71 (MQ=255)
                                aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACt                                 >  1:80436/1‑71 (MQ=255)
                                aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACt                                 >  1:1046115/1‑71 (MQ=255)
                                aTTTCTTGTGTATCAGACAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACt                                 >  1:25285/1‑71 (MQ=255)
                                aTTTCTTGTGTATCAGACAATAAGCATTCATTCAACACCTTTAGAAATAATCAAAACACAGGTATTCCAc                                  >  1:2663423/1‑70 (MQ=255)
                                          tATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAatata                       >  1:2084791/1‑71 (MQ=255)
                                          tATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAatata                       >  1:3303031/1‑71 (MQ=255)
                                                aCAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:2202473/61‑1 (MQ=255)
                                                aCAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:1134451/61‑1 (MQ=255)
                                                aCAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:1250307/61‑1 (MQ=255)
                                                aCAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:683021/61‑1 (MQ=255)
                                                aCAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:3020221/61‑1 (MQ=255)
                                                aCAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:2783627/61‑1 (MQ=255)
                                                 cAATAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTaa                           <  1:2513911/60‑1 (MQ=255)
                                                 cAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTcaca                 >  1:2161541/1‑70 (MQ=255)
                                                    tAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATTTATTCACatat              >  1:1872333/1‑70 (MQ=255)
                                                    tAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTcac                  >  1:3245468/1‑66 (MQ=255)
                                                    tAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACatat              >  1:397715/1‑70 (MQ=255)
                                                    tAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACatat              >  1:885337/1‑70 (MQ=255)
                                                    tAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACatat              >  1:2887240/1‑70 (MQ=255)
                                                    tAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACatat              >  1:1601477/1‑70 (MQ=255)
                                                    tAAGCATTCATTCAAGACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACatat              >  1:2174277/1‑70 (MQ=255)
                                                                caAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGaataaa  <  1:1254417/70‑1 (MQ=255)
                                                                caAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGaataaa  <  1:1094170/70‑1 (MQ=255)
                                                                caAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGaataaa  <  1:2050959/70‑1 (MQ=255)
                                                                caAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGaataaa  <  1:1972256/70‑1 (MQ=255)
                                                                caAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGaataaa  <  1:3128866/70‑1 (MQ=255)
                                                                   |                                                                  
AAATATCATTTTTTAACGATAAAAAGAGTGTTATTTCTTGTGTATCAGACAATAAGCATTCATTCAAAACCTTTAGAAATAATCAAAACACAGGTATTCCACTGGTTAATATATTCACATATGAAATGAATAAA  >  W3110S.gb/3135099‑3135232

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A