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 2,827,128 T→G 48.0% intergenic (‑110/+6) cutA ← / ← dcuA copper binding protein, copper sensitivity/C4‑dicarboxylate antiporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,827,1280TG48.0% ‑4.1 / 59.8 50intergenic (‑110/+6)cutA/dcuAcopper binding protein, copper sensitivity/C4‑dicarboxylate antiporter
Reads supporting (aligned to +/- strand):  ref base T (8/18);  new base G (22/2);  total (30/20)
Fisher's exact test for biased strand distribution p-value = 1.04e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.95e-01

ACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACACC  >  minE/2827060‑2827187
                                                                    |                                                           
aCTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGAtt                                                             >  1:1152129/1‑69 (MQ=255)
aCTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGAtt                                                             >  1:1180575/1‑69 (MQ=255)
  tataCAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTg                                                            <  1:2973109/68‑1 (MQ=255)
  tataCAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTg                                                            <  1:201300/68‑1 (MQ=255)
         cggccggGGGAAGGATGTTAGTCGGCGGGAAAGAACGCGGGGCGTGAACGCCCCGCGATTg                                                            <  1:3235957/61‑1 (MQ=255)
           gacggGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAg                                                  <  1:1824026/69‑1 (MQ=255)
           gacggGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAg                                                  <  1:1466991/69‑1 (MQ=255)
            acggGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAg                                                  <  1:3405454/68‑1 (MQ=255)
            acggGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAg                                                  <  1:552107/68‑1 (MQ=255)
                      gATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTa                                        >  1:2430903/1‑68 (MQ=255)
                      gATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTa                                        >  1:2216165/1‑68 (MQ=255)
                      gATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTa                                        >  1:2545313/1‑68 (MQ=255)
                      gATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTa                                        >  1:2894791/1‑68 (MQ=255)
                             gTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTg                                                            <  1:2696403/41‑1 (MQ=255)
                                         gaaagCGGGGCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCa                    <  1:366607/69‑1 (MQ=255)
                                         gaaagCGGGGCGTGAACGCCCCGCGATGGGTCATTACAGCATGAAGCTAccc                                     <  1:3431399/52‑1 (MQ=255)
                                                gggCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCa                    <  1:2410737/62‑1 (MQ=255)
                                                gggCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCa                    <  1:2316294/62‑1 (MQ=255)
                                                       aaCGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCaa      <  1:1757448/69‑1 (MQ=255)
                                                       aaCGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCaa      >  1:271253/1‑69 (MQ=255)
                                                       aaCGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCaa      >  1:2735703/1‑69 (MQ=255)
                                                       aaCGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCaa      >  1:1455565/1‑69 (MQ=255)
                                                       aaCGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCaa      >  1:731070/1‑69 (MQ=255)
                                                        aCGCCCCGCGATGGGTCATTACAGCATGAAGCTAccc                                     <  1:639918/37‑1 (MQ=255)
                                                           ccccGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  <  1:562780/69‑1 (MQ=255)
                                                           ccccGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  <  1:2615339/69‑1 (MQ=255)
                                                           ccccGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  <  1:1463415/69‑1 (MQ=255)
                                                           ccccGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  <  1:133271/69‑1 (MQ=255)
                                                           ccccGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  <  1:1125829/69‑1 (MQ=255)
                                                            cccGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  <  1:871833/68‑1 (MQ=255)
                                                             ccGCGATGGGTCATTACAGGATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:2573130/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGCAGCTACCCAGc                                  >  1:1653500/1‑35 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAATCAAACGGCCAGGGCAACAcc  >  1:1054498/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:906410/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:718179/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:402438/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:80865/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:339044/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:3343571/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:3223850/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:3044705/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:2869715/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:2834582/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:276293/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:2328466/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:2307778/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:2303997/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:1444504/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:1127669/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:1095756/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:1063012/1‑67 (MQ=255)
                                                             ccGCGATGGGTCATTACAGCATGAAGCCACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACAcc  >  1:1857297/1‑67 (MQ=255)
                                                                    |                                                           
ACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAGCATGAAGCTACCCAGCACGAAGCCGAAGCAAACGGCCAGGGCAACACC  >  minE/2827060‑2827187

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