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 F3 I0 R1 328 90.1 2317887 85.2% 1974839 62.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,077,998 T→C 100% L14L (TTA→TTG)  ydhU ← predicted cytochrome

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,077,9980TC80.3% 155.2 / 32.7 76L14L (TTA→TTG) ydhUpredicted cytochrome
Reads supporting (aligned to +/- strand):  ref base T (10/5);  new base C (61/0);  total (71/5)
Fisher's exact test for biased strand distribution p-value = 1.63e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.91e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAACCACACCGGCCAAAATTCGGGAGTGAACTGTGGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAG  >  minE/1077950‑1078020
                                                |                      
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:398564/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2123999/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2132776/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2211967/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:921070/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2239356/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2245847/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2265271/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2281000/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2306056/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:245573/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:262396/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:282541/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:91818/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:362880/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:395502/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:2020940/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:898791/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:441271/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:451690/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:457020/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:488725/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:89151/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:526474/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:628719/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:639474/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:647632/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:673685/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:674179/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:851472/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:744643/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:791786/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:9724/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1036394/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1121131/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1150103/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1169885/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1188852/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1386950/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:976445/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1475439/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1491533/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1501565/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1511004/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1525767/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1590814/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1954656/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:164602/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:167726/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1696490/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1954058/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1928093/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1730588/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:190471/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1767658/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1768778/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:177620/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:180994/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1815699/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTGTGGAACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:40683/1‑66 (MQ=255)
cAACCACACCGGCCAAAATTGGGGGGTGAACTCTGGCACATAGTTCGCCAACTGGCTCTGAAACTg       >  1:1606520/1‑66 (MQ=255)
   ccACACCGGCCAAAATTCGGGAGTGAACTGTGGCACATAGTTCGCTAACTGGCTCTGAAACTGTTc    <  1:1753869/66‑1 (MQ=255)
                              cTGTGGCACATAGTTCGCTAACTGGCTCTGAAACTGTTc    <  1:1164816/39‑1 (MQ=255)
                              cTGTGGCACATAGTTCGCTAACTGGCTCTGAAACTGTTc    <  1:1555263/39‑1 (MQ=255)
                              cTGTGGCACATAGTTCGCTAACTGGCTCTGAAACTGTTc    <  1:1568111/39‑1 (MQ=255)
                               tgtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTc    <  1:2188906/38‑1 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCa   >  1:995950/1‑38 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:762839/1‑39 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:724744/1‑39 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:519963/1‑39 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:406440/1‑39 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:3050/1‑39 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:2232945/1‑39 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:1605622/1‑39 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:147538/1‑39 (MQ=255)
                                gtgGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAg  >  1:1004368/1‑39 (MQ=255)
                                                |                      
CAACCACACCGGCCAAAATTCGGGAGTGAACTGTGGCACATAGTTCGCTAACTGGCTCTGAAACTGTTCAG  >  minE/1077950‑1078020

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A