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 2,418,876 T→C 24.2% K379K (AAA→AAG)  wzyE ← predicted Wzy protein involved in ECA polysaccharide chain elongation

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,418,8760TC24.2% 132.0 / 37.7 107K379K (AAA→AAG) wzyEpredicted Wzy protein involved in ECA polysaccharide chain elongation
Reads supporting (aligned to +/- strand):  ref base T (37/44);  new base C (18/8);  total (55/52)
Fisher's exact test for biased strand distribution p-value = 4.40e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

Only 100 of 111 total aligned reads displayed.

GCCCTTCACGCGCCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCATTTGATGATCAGACCA  >  minE/2418809‑2418942
                                                                   |                                                                  
gCCCTTCACGCGCCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCtt                                                                   <  1:2147073/69‑1 (MQ=255)
  ccTTCACGCGCCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCtt                                                                   >  1:705346/1‑67 (MQ=255)
  ccTTCACGCGCCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCtt                                                                   >  1:213412/1‑67 (MQ=255)
  ccTTCACGCGCCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCtt                                                                   >  1:1910767/1‑67 (MQ=255)
      cACGCGCCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:578266/1‑69 (MQ=255)
      cACGCGCCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:53123/1‑69 (MQ=255)
         gcgcCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGAt                                                          <  1:1030816/69‑1 (MQ=255)
         gcgcCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGAt                                                          <  1:1713981/69‑1 (MQ=255)
         gcgcCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGAt                                                          <  1:2963127/69‑1 (MQ=255)
         gcgcCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGAt                                                          <  1:1823713/69‑1 (MQ=255)
         gcgcCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGAt                                                          <  1:1560283/69‑1 (MQ=255)
         gcgcCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGAt                                                          <  1:2482366/69‑1 (MQ=255)
         gcgcCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGAt                                                          <  1:124713/69‑1 (MQ=255)
         gcgcCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGAt                                                          <  1:2369906/69‑1 (MQ=255)
             cAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAgg                                                      <  1:3324369/69‑1 (MQ=255)
             cAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAgg                                                      <  1:2432164/69‑1 (MQ=255)
             cAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAgg                                                      <  1:2717515/69‑1 (MQ=255)
              aGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGc                                                     >  1:2460556/1‑69 (MQ=255)
              aGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGc                                                     >  1:2861628/1‑69 (MQ=255)
                      cATATTGAAGATCGCCGCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:31780/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:2458322/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:1898364/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:1869662/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:2103309/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:2178073/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:3062788/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:2927222/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:1786531/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:3246833/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:1401118/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:1137647/49‑1 (MQ=255)
                      cATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:1122923/49‑1 (MQ=255)
                         atTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGc                                           <  1:1370078/68‑1 (MQ=255)
                         atTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGc                                           <  1:1317808/68‑1 (MQ=255)
                         atTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGc                                           <  1:1186567/68‑1 (MQ=255)
                         atTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGc                                           <  1:694908/68‑1 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAg                                                              >  1:1499886/1‑48 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:2328238/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:832739/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:2359501/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:728818/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:556194/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:3197775/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:913718/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:2198559/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:1058103/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:1914798/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:1431290/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:1603950/1‑49 (MQ=255)
                          ttGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGc                                                             >  1:1678668/1‑49 (MQ=255)
                           tGAAGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTcg                                                  >  1:1462487/1‑59 (MQ=255)
                           tGAAGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGccc                                         >  1:896083/1‑68 (MQ=255)
                           tGAAGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGccc                                         >  1:1223014/1‑68 (MQ=255)
                           tGAAGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGccc                                         >  1:541787/1‑68 (MQ=255)
                           tGAAGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGccc                                         >  1:2671785/1‑68 (MQ=255)
                              aGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGc                                      <  1:101314/68‑1 (MQ=255)
                              aGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGc                                      <  1:840325/68‑1 (MQ=255)
                              aGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGc                                      <  1:3149250/68‑1 (MQ=255)
                              aGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGc                                      <  1:2701189/68‑1 (MQ=255)
                              aGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGc                                      <  1:2378216/68‑1 (MQ=255)
                              aGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGc                                      <  1:2672245/68‑1 (MQ=255)
                              aGATCGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGc                                      <  1:2498539/68‑1 (MQ=255)
                                aTCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTta                                                                 <  1:3023527/39‑1 (MQ=255)
                                aTCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCa                                   <  1:244504/69‑1 (MQ=255)
                                aTCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCa                                   <  1:1036896/69‑1 (MQ=255)
                                aTCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCa                                   <  1:3255101/69‑1 (MQ=255)
                                aTCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCa                                   <  1:2587716/69‑1 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:320916/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:1103389/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:1921868/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:1258592/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:352404/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:1898872/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:769780/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:3243062/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:3073821/1‑67 (MQ=255)
                                  cGCCCCGAAGCAGAAACTGTGCAATATCGCAGCCTTATAGCGATTAGTCTCGCGGTTGCCCAGCTCa                                   >  1:1463813/1‑67 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGAtt                                                         >  1:111030/1‑35 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        <  1:371811/36‑1 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        >  1:893014/1‑36 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        >  1:1791135/1‑36 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        <  1:2873551/36‑1 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        >  1:1741160/1‑36 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        <  1:2930695/36‑1 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        >  1:3031214/1‑36 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        >  1:162790/1‑36 (MQ=255)
                                            cAGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        <  1:3138830/36‑1 (MQ=255)
                                             aGAAACTGTGCAATATCGCAGCTTTATAGCGATTa                                                        <  1:779266/35‑1 (MQ=255)
                                                            tCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACa                               >  1:350332/1‑45 (MQ=255)
                                                            tCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCa                  <  1:501810/58‑1 (MQ=255)
                                                            tCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCa                  <  1:2098932/58‑1 (MQ=255)
                                                            tCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCa                  <  1:1178281/58‑1 (MQ=255)
                                                            tCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCATTTGATGATCa       >  1:1838767/1‑69 (MQ=255)
                                                            tCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCATTTGATGATCa       >  1:3280457/1‑69 (MQ=255)
                                                            tCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCATTTGATGATCa       >  1:1876685/1‑69 (MQ=255)
                                                            tCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCATTTGATGATCa       >  1:2687182/1‑69 (MQ=255)
                                                              gCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCa                                   >  1:2983203/1‑39 (MQ=255)
                                                              gCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCa                                   >  1:2163576/1‑39 (MQ=255)
                                                                 gCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCATTTGATGATCAGacca  >  1:2889336/1‑69 (MQ=255)
                                                                 gCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCATTTGATGATCAGacca  >  1:2212473/1‑69 (MQ=255)
                                                                   |                                                                  
GCCCTTCACGCGCCAGCACGATCATATTGAAGATCGCCCCAAAGCAGAAACTGTGCAATATCGCAGCTTTATAGCGATTAGGCTCGCGGTTGCCCAGCTCATACAGCCAGTCGAACCATTTGATGATCAGACCA  >  minE/2418809‑2418942

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