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 2,281,141 C→T 34.3% A60A (GCG→GCA)  fabR ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,281,1410CT34.3% 73.2 / 52.3 96A60A (GCG→GCA) fabRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (38/25);  new base T (18/15);  total (56/40)
Fisher's exact test for biased strand distribution p-value = 6.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.81e-02

GTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTAAAT  >  minE/2281082‑2281207
                                                           |                                                                  
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:2316524/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:2266472/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:3228423/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:3245033/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:2484410/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:1858548/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:1846304/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:2630775/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCt                                                                 >  1:458471/1‑63 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCAcgc                                                           >  1:2766601/1‑69 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCAcgc                                                           >  1:3173869/1‑69 (MQ=255)
gTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCAcgc                                                           >  1:1534153/1‑69 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGTGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:248123/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:597528/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:1182003/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:333365/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:1113631/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:2187115/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:85500/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:2935989/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:2278607/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:1844131/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:2674651/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:465343/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:254225/69‑1 (MQ=255)
          gTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCAc                                                 <  1:2988387/69‑1 (MQ=255)
            tCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCAc                                                 >  1:216139/1‑67 (MQ=255)
            tCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACg                                                >  1:3100874/1‑68 (MQ=255)
            tCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACg                                                >  1:2598181/1‑68 (MQ=255)
            tCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACg                                                >  1:2659553/1‑68 (MQ=255)
            tCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACg                                                >  1:632715/1‑68 (MQ=255)
            tCGTCTACGTCGCGGAAAAGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACg                                                >  1:1913589/1‑68 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCACGCGCCACTTCACGCAAACt                                          <  1:2372929/69‑1 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCaaa                                            >  1:401290/1‑67 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCaaa                                            >  1:1915128/1‑67 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCaaa                                            >  1:667694/1‑67 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCaaa                                            >  1:3052739/1‑67 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCaaa                                            >  1:3162420/1‑67 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCaaa                                            >  1:2409332/1‑67 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACt                                          <  1:3255355/69‑1 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACt                                          <  1:2290371/69‑1 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACt                                          <  1:1799932/69‑1 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACt                                          <  1:62201/69‑1 (MQ=255)
                 tACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACt                                          <  1:1039776/69‑1 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCa                                        >  1:556983/1‑65 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:3173422/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:880160/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:3305416/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:540927/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:656851/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:737224/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:850885/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:1039487/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:2893725/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:2797450/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:2657642/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:1732697/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:2524228/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:2023234/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:241400/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:216519/1‑66 (MQ=255)
                       gcgGAAATGCCGATAAAAAGAGGTCGGAGCAATGCCTGCTTCTCGTGCCACTTCACGCAAACTCAg                                       >  1:1954711/1‑66 (MQ=255)
                               gCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCTCCACtt                                                    <  1:6349/45‑1 (MQ=255)
                               gCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACtt                                                    <  1:106508/45‑1 (MQ=255)
                               gCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACtt                                                    <  1:824326/45‑1 (MQ=255)
                               gCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACtt                                                    <  1:1198273/45‑1 (MQ=255)
                               gCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACtt                                                    <  1:1689145/45‑1 (MQ=255)
                               gCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACtt                                                    <  1:3112389/45‑1 (MQ=255)
                               gCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACtt                                                    <  1:2349136/45‑1 (MQ=255)
                                ccGATAAAAAGAGGTGGGAGCAATGCGCGCTTCACGCGCCACtt                                                    <  1:2711960/44‑1 (MQ=255)
                                 cGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACt                                          <  1:1310662/53‑1 (MQ=255)
                                     aaaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCg                        >  1:736561/1‑67 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:2326378/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:2043932/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:2466362/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:3267658/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:1995905/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:2572257/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:3177167/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:2989791/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:1537915/1‑69 (MQ=255)
                                      aaaaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc                     >  1:1433990/1‑69 (MQ=255)
                                        aaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAg                   <  1:802762/69‑1 (MQ=255)
                                        aaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAg                   <  1:1295181/69‑1 (MQ=255)
                                        aaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAg                   <  1:3001853/69‑1 (MQ=255)
                                        aaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAg                   <  1:1741429/69‑1 (MQ=255)
                                        aaGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAg                   <  1:3031461/69‑1 (MQ=255)
                                                ggAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAg                   <  1:2687557/61‑1 (MQ=255)
                                                      aTGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTa     <  1:1087859/69‑1 (MQ=255)
                                                      aTGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTa     <  1:1149200/69‑1 (MQ=255)
                                                      aTGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTa     <  1:279804/69‑1 (MQ=255)
                                                      aTGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTa     <  1:760401/69‑1 (MQ=255)
                                                       tGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTa     <  1:2772153/68‑1 (MQ=255)
                                                        gCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTaaa   >  1:135450/1‑69 (MQ=255)
                                                        gCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTaaa   >  1:747997/1‑69 (MQ=255)
                                                        gCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTaaa   >  1:201322/1‑69 (MQ=255)
                                                         cccGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTAAAt  >  1:1286975/1‑69 (MQ=255)
                                                         cccGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTAAAt  >  1:3207469/1‑69 (MQ=255)
                                                           |                                                                  
GTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTCAGCACTTAATTGGCTAAAT  >  minE/2281082‑2281207

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