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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,003,978 G→A 34.1% V23V (GTC→GTT)  hybD ← predicted maturation element for hydrogenase 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,003,9780GA34.1% 96.5 / 65.4 120V23V (GTC→GTT) hybDpredicted maturation element for hydrogenase 2
Reads supporting (aligned to +/- strand):  ref base G (60/19);  new base A (20/21);  total (80/40)
Fisher's exact test for biased strand distribution p-value = 4.09e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.53e-01

Only 100 of 120 total aligned reads displayed.

CCCGCCGTGCCGCCATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCC  >  minE/2003913‑2004027
                                                                 |                                                 
cccGCCGTGCCGCCATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACa                                                <  1:1295237/69‑1 (MQ=255)
         ccgccATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGcaca                                       <  1:3253304/69‑1 (MQ=255)
         ccgccATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGcaca                                       <  1:179399/69‑1 (MQ=255)
         ccgccATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGcaca                                       <  1:385163/69‑1 (MQ=255)
         ccgccATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGcaca                                       <  1:436625/69‑1 (MQ=255)
         ccgccATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGcaca                                       <  1:3156105/69‑1 (MQ=255)
         ccgccATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGcaca                                       <  1:2042047/69‑1 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCg                                           >  1:1909828/1‑57 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCg                                           >  1:842203/1‑57 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCg                                           >  1:3224358/1‑57 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCg                                           >  1:2936857/1‑57 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCg                                           >  1:2010765/1‑57 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATgg                                >  1:1990700/1‑68 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGc                               >  1:3415826/1‑69 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGc                               >  1:1940955/1‑69 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGc                               >  1:411056/1‑69 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGc                               >  1:3308594/1‑69 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGc                               >  1:1249352/1‑69 (MQ=255)
                 gAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGc                               >  1:2016652/1‑69 (MQ=255)
                     aTCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCa                           >  1:1496874/1‑69 (MQ=255)
                     aTCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCa                           >  1:808018/1‑69 (MQ=255)
                     aTCTCAACATAATCCGGCAGAATGTATCGATGCTCTAAAGCTTCGACaa                                               >  1:2869659/1‑49 (MQ=255)
                       ctcAACATAATCCGGGAGAATGTATCGTTGCTCTAACGCTTCGACAATCCg                                           <  1:835083/51‑1 (MQ=255)
                       ctcAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCg                                           <  1:2367569/51‑1 (MQ=255)
                       ctcAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCg                                           <  1:1858850/51‑1 (MQ=255)
                       ctcAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACAcc                                     >  1:24536/1‑57 (MQ=255)
                       ctcAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACAcc                                     >  1:1198116/1‑57 (MQ=255)
                       ctcAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATc                         >  1:2213584/1‑69 (MQ=255)
                       ctcAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATc                         >  1:1139307/1‑69 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTGAACAATCCg                                           >  1:3113681/1‑46 (MQ=39)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:2109783/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:1073347/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:3059143/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:2976004/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:2401386/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:2515396/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:1904406/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:1561552/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:1413897/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:627711/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:2094739/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:135859/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCg                                           >  1:1357873/1‑46 (MQ=255)
                            cATAATCCGGCAGAATGTATCGTTCCTCTAACGCTTCAACAATCCg                                           >  1:1277437/1‑46 (MQ=255)
                                aTCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCaa                >  1:1530712/1‑69 (MQ=255)
                                aTCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCaa                >  1:623377/1‑69 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:740253/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:2765533/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:2769858/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:2813568/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:946668/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:895971/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:2916051/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:3122433/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:441330/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:3263626/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:2718654/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:2038475/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:1339629/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:1375119/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:1130839/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:2214042/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:1569149/69‑1 (MQ=255)
                                  ccGGCAGAATGTATCGTTGCTCTAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:2259098/69‑1 (MQ=255)
                                   cGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAat             <  1:33744/69‑1 (MQ=255)
                                   cGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAat             <  1:2233952/69‑1 (MQ=255)
                                    ggCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAat             <  1:2299550/68‑1 (MQ=255)
                                       aGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTg         <  1:2238466/69‑1 (MQ=255)
                                         aaTGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGcc       <  1:300604/69‑1 (MQ=255)
                                         aaTGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGcc       <  1:3193655/69‑1 (MQ=255)
                                         aaTGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGcc       <  1:673148/69‑1 (MQ=255)
                                          aTGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCt                              >  1:343256/1‑45 (MQ=255)
                                          aTGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCg      >  1:144011/1‑69 (MQ=255)
                                          aTGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCg      >  1:919128/1‑69 (MQ=255)
                                          aTGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCg      >  1:2560622/1‑69 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGAt                                  >  1:2174299/1‑40 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGa     >  1:1414742/1‑69 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGa     >  1:642278/1‑69 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGa     >  1:2045703/1‑69 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGa     >  1:746372/1‑69 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGa     >  1:2085860/1‑69 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGa     >  1:220549/1‑69 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGa     >  1:2490816/1‑69 (MQ=255)
                                           tGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGa     >  1:2509953/1‑69 (MQ=255)
                                             tATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCgcc    >  1:1200607/1‑66 (MQ=255)
                                             tATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAcc   >  1:2649322/1‑69 (MQ=255)
                                             tATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAcc   >  1:3332220/1‑69 (MQ=255)
                                             tATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAcc   >  1:325837/1‑69 (MQ=255)
                                             tATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAc    >  1:2365056/1‑68 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGc                               >  1:1140996/1‑37 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAata            >  1:1364155/1‑56 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAccc  >  1:1418221/1‑66 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAccc  >  1:1529689/1‑66 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAccc  >  1:3430182/1‑66 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAccc  >  1:329704/1‑66 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAccc  >  1:865807/1‑66 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAccc  >  1:2527840/1‑66 (MQ=255)
                                                 gTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAccc  >  1:1064339/1‑66 (MQ=255)
                                                        tAACGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:915195/47‑1 (MQ=255)
                                                           cGCTTCAACAATCCGCACACCGATGGCTTCATCGGTCAGCaaaa              <  1:3058630/44‑1 (MQ=255)
                                                                 |                                                 
CCCGCCGTGCCGCCATCGAGGATCTCAACATAATCCGGCAGAATGTATCGTTGCTCTAACGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCC  >  minE/2003913‑2004027

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