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
A4 F28 I2 R2 42 122.2 1899532 52.7% 1001053 56.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 2,705,644 (A)5→6 coding (462/837 nt) dam → DNA adenine methylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,705,6391.A99.2% 398.8 / ‑3.0 120coding (457/837 nt)damDNA adenine methylase
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base A (0/119);  total (0/120)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

Only 100 of 120 total aligned reads displayed.

AAGCAGAGTTGTATCACTTCGCTG‑AA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTA  >  minE/2705616‑2705676
                        |                                      
aaGCAGAGTTGTATCACTTCTCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGGCTTa  <  1:1260688/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:274745/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:586114/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:585077/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:541086/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:526619/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:445575/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:422146/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:388109/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:377475/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:353300/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:319549/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:312417/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:608879/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:266468/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:259730/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:232811/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:221790/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:22092/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:201696/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1881899/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:184578/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1819122/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1817018/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1811970/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:866200/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:982406/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:972668/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:957799/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:945846/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:942172/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:933663/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:912234/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:907094/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:901915/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:894923/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:892316/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:596546/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:855252/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:832053/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:812155/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:797430/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:782185/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:759526/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:740967/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:664543/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:64904/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:635981/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1003525/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1095472/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:18000/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1306074/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1302068/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:129803/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1286089/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1220998/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1209561/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1186500/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1154061/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1141692/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1102529/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1098498/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1337489/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:109053/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1078099/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1067476/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1061855/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1059697/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1058067/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1053556/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1030650/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1014566/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1010223/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1001459/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1762635/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:168847/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1606292/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1570771/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1564312/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1343499/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1508834/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1721437/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1500685/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1489419/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1461196/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1769047/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1774238/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1433616/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:17831/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:137833/62‑1 (MQ=255)
aaGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTATCTATTGTGAGTCTTa  <  1:1715780/62‑1 (MQ=255)
 aGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1521923/61‑1 (MQ=255)
 aGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1519405/61‑1 (MQ=255)
 aGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:790487/61‑1 (MQ=255)
 aGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1460138/61‑1 (MQ=255)
 aGCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1451871/61‑1 (MQ=255)
  gCAGAGTTGTATCTCTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1805472/60‑1 (MQ=255)
  gCAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1502176/60‑1 (MQ=255)
   cAGAGTTGTATCACTTCGCTGAAA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:632624/59‑1 (MQ=255)
                    gCTG‑AATAAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTa  <  1:1646071/42‑1 (MQ=38)
                        |                                      
AAGCAGAGTTGTATCACTTCGCTG‑AA‑AAAGCGCAGAATGCCTTTTTCTATTGTGAGTCTTA  >  minE/2705616‑2705676

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