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 1,156,730 G→A 56.8% L232L (CTC→CTT)  astD ← succinylglutamic semialdehyde dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,156,7300GA56.8% 19.9 / 68.2 88L232L (CTC→CTT) astDsuccinylglutamic semialdehyde dehydrogenase
Reads supporting (aligned to +/- strand):  ref base G (11/27);  new base A (36/14);  total (47/41)
Fisher's exact test for biased strand distribution p-value = 8.72e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.22e-01

AATTAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGA  >  minE/1156673‑1156790
                                                         |                                                            
aaTTAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGa                                                     >  1:1926951/1‑67 (MQ=255)
aaTTAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGAt                                                    >  1:981588/1‑68 (MQ=255)
aaTTAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGAt                                                    >  1:461910/1‑68 (MQ=255)
aaTTAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCCGCTGACCGGAGAGCTGGCGAt                                                    >  1:2506783/1‑68 (MQ=255)
  ttAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGc                                                  <  1:1840506/68‑1 (MQ=255)
  ttAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGc                                                  <  1:2350972/68‑1 (MQ=255)
  ttAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGc                                                  <  1:250277/68‑1 (MQ=255)
  ttAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGc                                                  <  1:2761470/68‑1 (MQ=255)
  ttAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGc                                                  <  1:3383425/68‑1 (MQ=255)
  ttAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGc                                                  <  1:829478/68‑1 (MQ=255)
          ttattaCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGgaga                                                             <  1:2766198/49‑1 (MQ=255)
          ttattaCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGgaga                                                             <  1:1408346/49‑1 (MQ=255)
          ttattaCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGgaga                                                             <  1:2601082/49‑1 (MQ=255)
          ttattaCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGgaga                                                             <  1:6661/49‑1 (MQ=255)
          ttattaCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGgaga                                                             <  1:1217841/49‑1 (MQ=255)
           tattaCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGgaga                                                             <  1:516551/48‑1 (MQ=255)
              taCCGTCCATCTCAAGGGCGAGAATTTTCTCCGTCTGACCGGAAAGCTGGCGAt                                                    >  1:1176915/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGCCCGGAAAGCTGGCGAt                                                    >  1:3302998/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGgaga                                                             <  1:2307126/45‑1 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:548377/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:3301641/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:3307155/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:3385178/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:3399008/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:229575/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:2207937/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:3002457/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:487314/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:2164847/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:1306979/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:655638/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:744558/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:77094/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:2050710/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:2650410/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:2986621/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:909605/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:1656387/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:1885522/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:1850795/1‑54 (MQ=255)
              taCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAAAGCTGGCGAt                                                    >  1:2800649/1‑54 (MQ=255)
               aCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGt                                    >  1:2422717/1‑69 (MQ=255)
               aCCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGt                                    >  1:947890/1‑69 (MQ=255)
                         tcAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTg                                     >  1:2070120/1‑58 (MQ=255)
                         tcAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTa                          >  1:1846618/1‑69 (MQ=255)
                         tcAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTa                          >  1:3044311/1‑69 (MQ=255)
                              ggCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCt                           <  1:1546206/63‑1 (MQ=255)
                              ggCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCt                           <  1:874323/63‑1 (MQ=255)
                               gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:3429695/69‑1 (MQ=255)
                               gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:1264815/69‑1 (MQ=255)
                               gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:29931/69‑1 (MQ=255)
                               gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:2976295/69‑1 (MQ=255)
                               gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:1141960/69‑1 (MQ=255)
                               gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:218615/69‑1 (MQ=255)
                               gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:1979074/69‑1 (MQ=255)
                               gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:2816779/69‑1 (MQ=255)
                                cGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:1873004/68‑1 (MQ=255)
                                cGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa                    <  1:897004/68‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:3239420/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:2053038/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:341402/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:1341658/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:1585686/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:2182781/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:2149691/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:2123020/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:600942/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:2101168/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:2984110/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:1364929/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:696457/69‑1 (MQ=255)
                                  agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc                 <  1:2056916/69‑1 (MQ=255)
                                      ttttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCa             >  1:1654251/1‑69 (MQ=255)
                                       tttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCaa            <  1:3255002/69‑1 (MQ=255)
                                       tttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCa             <  1:2838037/68‑1 (MQ=255)
                                       tttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCa             <  1:262556/68‑1 (MQ=255)
                                       tttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCa             <  1:2889671/68‑1 (MQ=255)
                                        ttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCaaa           >  1:1303754/1‑69 (MQ=255)
                                                 tGACCGGAGAGCTGGCGATGCAACTGGTAGCCTTTATTGGCGCTACCGGTAAACAGCAAACCGTCgaga  <  1:1942759/69‑1 (MQ=255)
                                                 tGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCgaga  <  1:3375486/69‑1 (MQ=255)
                                                 tGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCgaga  <  1:2493957/69‑1 (MQ=255)
                                                 tGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCgaga  <  1:3145888/69‑1 (MQ=255)
                                                  gACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCTCTACCGGTAAACAGCAAACCGTCgaga  <  1:780244/68‑1 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:1927370/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:927418/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:1714821/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:2339395/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:1355029/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:3334779/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:1557868/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:3254600/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:3125445/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:2544320/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:2724894/1‑64 (MQ=255)
                                                     cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag   >  1:1367178/1‑64 (MQ=255)
                                                         |                                                            
AATTAGCGGATTATTACCGCCCATCTCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGA  >  minE/1156673‑1156790

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