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 1,465,518 G→A 34.8% I485I (ATC→ATT)  gyrA ← DNA gyrase (type II topoisomerase), subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,465,5180GA34.8% 63.0 / 47.3 86I485I (ATC→ATT) gyrADNA gyrase (type II topoisomerase), subunit A
Reads supporting (aligned to +/- strand):  ref base G (41/15);  new base A (14/16);  total (55/31)
Fisher's exact test for biased strand distribution p-value = 1.91e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.39e-01

CTCTTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGACCGGTCAGTT  >  minE/1465458‑1465579
                                                            |                                                             
ttctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:2340464/2‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:3323116/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:2460837/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:2158399/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:2485677/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:27643/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:2816511/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:323916/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:1749572/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:15160/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:1447484/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:900516/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:843404/1‑67 (MQ=255)
ctctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACACTTCCGCGATc                                                            >  1:3384485/1‑64 (MQ=255)
 tctTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATcc                                                      <  1:586007/69‑1 (MQ=255)
        ggATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCcagcag                                                 <  1:407669/67‑1 (MQ=255)
        ggATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCcagcag                                                 <  1:3335733/67‑1 (MQ=255)
        ggATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCcagcag                                                 <  1:1800352/67‑1 (MQ=255)
        ggATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCcagcag                                                 <  1:2069829/67‑1 (MQ=255)
        ggATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCcagcag                                                 <  1:812059/67‑1 (MQ=255)
         gATCACTTCCATCAGACGATAGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCcagcag                                                 <  1:893059/66‑1 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:932043/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:436942/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:2437432/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:2452089/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:2455906/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:3203131/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:550021/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:461897/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:3269194/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:2523649/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:380815/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:1301135/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:2253559/1‑57 (MQ=255)
          aTCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCAATCTGa                                                         >  1:2264655/1‑57 (MQ=255)
           tCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGctct                                             >  1:1631731/1‑68 (MQ=255)
           tCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCtt                                            >  1:2463547/1‑69 (MQ=255)
               ttCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTa                                        <  1:1992305/69‑1 (MQ=255)
               ttCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTa                                        <  1:1159180/69‑1 (MQ=255)
               ttCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTa                                        <  1:1410484/69‑1 (MQ=255)
               ttCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTa                                        <  1:1491632/69‑1 (MQ=255)
               ttCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTa                                        <  1:433732/69‑1 (MQ=255)
               ttCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTa                                        <  1:1699570/69‑1 (MQ=255)
               ttCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTa                                        <  1:2945208/69‑1 (MQ=255)
               ttCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTa                                        <  1:2184126/69‑1 (MQ=255)
                    tCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATtcg                                    >  1:2520590/1‑68 (MQ=255)
                     cAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATtcg                                    >  1:2093335/1‑67 (MQ=255)
                     cAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATtcg                                    >  1:2802163/1‑67 (MQ=255)
                     cAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATtcg                                    >  1:2837330/1‑67 (MQ=255)
                     cAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATtcg                                    >  1:2152409/1‑67 (MQ=255)
                     cAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATtc                                     >  1:665759/1‑66 (MQ=255)
                      aGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:257714/1‑45 (MQ=255)
                      aGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:3403245/1‑45 (MQ=255)
                      aGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:2166572/1‑45 (MQ=255)
                      aGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:1593451/1‑45 (MQ=255)
                      aGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:3163049/1‑45 (MQ=255)
                      aGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:3018383/1‑45 (MQ=255)
                      aGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGa                                                         >  1:1221108/1‑45 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:2254855/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:2194297/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:1260433/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:420037/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:85955/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:2334683/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:2681146/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:2050429/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:1700708/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:2850819/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:2035413/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:3165261/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:1123723/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:2963304/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:3093305/52‑1 (MQ=255)
                                       aaGAATACGCAACAGTTCCGCAATCTGATCCAGCAGCTCTTTGTATtcgtcg                                 <  1:3101065/52‑1 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGa            >  1:365010/1‑68 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:1350761/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:1169783/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:866750/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:669269/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:1308283/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:3431471/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:534578/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:2423863/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:1600293/1‑69 (MQ=255)
                                            tACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGAc           >  1:3432675/1‑69 (MQ=255)
                                                       tCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGACCGGTCAGtt  >  1:1717515/1‑67 (MQ=255)
                                                            |                                                             
CTCTTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGACCGGTCAGTT  >  minE/1465458‑1465579

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