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 1,261,587 T→C 21.9% A154A (GCA→GCG)  torY ← TMAO reductase III (TorYZ), cytochrome c‑type subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,261,5870TC21.9% 172.7 / 38.1 127A154A (GCA→GCG) torYTMAO reductase III (TorYZ), cytochrome c‑type subunit
Reads supporting (aligned to +/- strand):  ref base T (41/58);  new base C (11/17);  total (52/75)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 129 total aligned reads displayed.

TTATTTCTGGCGGAAAATGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATGGCATCAAAAGAATG  >  minE/1261523‑1261652
                                                                |                                                                 
ttATTTCTGGCGGAAAATGGGCAATGCCTTTATGGCAATCGATACAGGTTTCGCCGTCCTTTTGCGCtt                                                               >  1:1051863/1‑69 (MQ=38)
ttATTTCTGGCGGAAAATGGGCAATGCCTTTATGGCAATCGATACAGGTTTCGCCGTCCTTTTGCGCtt                                                               >  1:900877/1‑69 (MQ=38)
ttATTTCTGGCGGAAAATGGGCAATGCCTTTATGGCAATCGATACAGGTTTCGCCGTCCTTTTGCGCtt                                                               >  1:87904/1‑69 (MQ=38)
ttATTTCTGGCGGAAAATGGGCAATGCCTTTATGGCAATCGATACAGGTTTCGCCGTCCTTTTGCGCtt                                                               >  1:2645551/1‑69 (MQ=38)
ttATTTCTGGCGGAAAATGGGCAATGCCTTTATGGCAATCGATACAGGTTTCGCCGTCCTTTTGCGCtt                                                               >  1:2642443/1‑69 (MQ=38)
ttATTTCTGGCGGAAAATGGGCAATGCCTTTATGGCAATCGATACAGGTTTCGCCGTCCTTTTGCGCtt                                                               >  1:1009756/1‑69 (MQ=38)
ttATTTCTGGCGGAAAATGGGCAATGCCTTTATGGCAATCGATACAGGTTTCGCCGTCCTTTTGCGCtt                                                               >  1:155823/1‑69 (MQ=38)
           ggAAAATGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCa                                                      <  1:3218238/67‑1 (MQ=255)
           ggAAAATGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCa                                                      <  1:2724578/67‑1 (MQ=255)
           ggAAAATGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCa                                                      <  1:1924152/67‑1 (MQ=255)
            gAAAATGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCa                                                      <  1:1919767/66‑1 (MQ=255)
             aaaaTGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCa                                                      <  1:2454933/65‑1 (MQ=255)
               aaTGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTc                                                 <  1:2230145/68‑1 (MQ=255)
                aTGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCa                                                      <  1:3408365/62‑1 (MQ=255)
                  gggCAATGCCTTTATGACAATCGTTACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCa                                                      <  1:2542381/60‑1 (MQ=255)
                   ggCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCAtt                                                    <  1:1581090/61‑1 (MQ=255)
                   ggCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCAtt                                                    <  1:2867686/61‑1 (MQ=255)
                   ggCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCAtt                                                    <  1:273507/61‑1 (MQ=255)
                   ggCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCAtt                                                    <  1:1864529/61‑1 (MQ=255)
                   ggCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCAtt                                                    <  1:2004256/61‑1 (MQ=255)
                   ggCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCAtt                                                    <  1:1930398/61‑1 (MQ=255)
                         gCCTTTATGACAATCGATACAGGTTTCGCTGTGCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTc                                      >  1:452741/1‑69 (MQ=255)
                         gCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTc                                      >  1:1589090/1‑69 (MQ=255)
                         gCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTc                                      >  1:2797067/1‑69 (MQ=255)
                         gCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTc                                      >  1:2278379/1‑69 (MQ=255)
                         gCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTc                                      >  1:1498429/1‑69 (MQ=255)
                         gCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTc                                      >  1:2147229/1‑69 (MQ=255)
                         gCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTc                                      >  1:1673257/1‑69 (MQ=255)
                         gCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTc                                      >  1:164183/1‑69 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCtt                                                               >  1:2689861/1‑43 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCtt                                                               >  1:2778579/1‑43 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCtt                                                               >  1:3355270/1‑43 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCtt                                                               >  1:3289363/1‑43 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCtt                                                               >  1:2132376/1‑43 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCtt                                                               >  1:2875594/1‑43 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:2517097/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:1954025/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:266747/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:2967106/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:3393310/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:1193863/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:46282/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:818002/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:94503/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:1531152/63‑1 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCa                                     >  1:946690/1‑69 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCa                                     >  1:1369245/1‑69 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCa                                     >  1:2575002/1‑69 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCa                                     >  1:2916045/1‑69 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCa                                     >  1:750387/1‑69 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCa                                     >  1:686259/1‑69 (MQ=255)
                          ccTTTATGACAATCGATACAGGTTTCGCTGTCATTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:1591623/63‑1 (MQ=255)
                              tATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACttt                                 >  1:974629/1‑69 (MQ=255)
                              tATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACttt                                 >  1:1871243/1‑69 (MQ=255)
                              tATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACttt                                 >  1:641426/1‑69 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:3201718/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:2110960/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:3407943/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:1854315/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:1972612/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:711717/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:872618/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:1167448/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:1360/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:887144/69‑1 (MQ=255)
                                     aTCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:242549/69‑1 (MQ=255)
                                      tCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGc                          <  1:1285627/68‑1 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        <  1:795130/69‑1 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:1954731/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:1163729/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        <  1:3293300/69‑1 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:2119464/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:124176/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:3216152/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:3172832/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:1407549/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:2479872/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        <  1:1308617/69‑1 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        >  1:2820316/1‑69 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCaa                        <  1:2326376/69‑1 (MQ=255)
                                       cGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCa                         >  1:2382339/1‑68 (MQ=255)
                                           aCAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATc                    <  1:2532879/69‑1 (MQ=255)
                                           aCAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATc                    <  1:468206/69‑1 (MQ=255)
                                           aCAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATc                    <  1:2342033/69‑1 (MQ=255)
                                                 ttCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCa                                           <  1:3156575/40‑1 (MQ=255)
                                                          cTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATGGCATCAAAAg      <  1:152493/68‑1 (MQ=255)
                                                          cTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATGGCATCAAAAg      <  1:1720612/68‑1 (MQ=255)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGTGGCAATATCCATg                <  1:2461713/55‑1 (MQ=255)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:2813530/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:2763150/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:1671270/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:3197570/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:386739/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:2948907/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:3051047/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:3091505/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:3128263/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:2426670/55‑1 (MQ=39)
                                                             ttGCGCTTTATTATGCATCTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATg                <  1:20574/55‑1 (MQ=38)
                                                              tgtgCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATGGCATCAAAAGAATg  >  1:2279123/1‑68 (MQ=255)
                                                                |                                                                 
TTATTTCTGGCGGAAAATGGGCAATGCCTTTATGACAATCGATACAGGTTTCGCTGTCCTTTTGTGCTTTGTTATGCATTTTCTGCGCAGATTCACTTTGCGAGGCAATATCCATGGCATCAAAAGAATG  >  minE/1261523‑1261652

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