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
A1 F28 I3 R2 68 0.0 1607493 93.4% 1501398 66.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,819,255 A→G T471T (ACT→ACC)  alaS ← alanyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,819,2550AG90.8% 432.1 / 25.3 142T471T (ACT→ACC) alaSalanyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base A (0/13);  new base G (129/0);  total (129/13)
Fisher's exact test for biased strand distribution p-value = 1.15e-18
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.27e-01

Only 100 of 142 total aligned reads displayed.

GCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATGGTCATA  >  W3110S.gb/2819223‑2819287
                                |                                
gCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATg        <  1:342631/59‑1 (MQ=255)
gCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATg        <  1:1429077/59‑1 (MQ=255)
gCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATg        <  1:1357928/59‑1 (MQ=255)
gCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATg        <  1:1046134/59‑1 (MQ=255)
gCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATg        <  1:1257554/59‑1 (MQ=255)
gCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATg        <  1:1187806/59‑1 (MQ=255)
gCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATg        <  1:1176278/59‑1 (MQ=255)
gCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATg        <  1:926721/59‑1 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCGCTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1009/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGt                     >  1:701256/1‑38 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTc                   >  1:972872/1‑40 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAg                 >  1:1083626/1‑42 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTGATa  >  1:840121/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCAt   >  1:380163/1‑56 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCAt   >  1:96073/1‑56 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCAt   >  1:257253/1‑56 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCAt   >  1:1156311/1‑56 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCAt   >  1:1247775/1‑56 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:505186/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:612121/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:587119/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:560207/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:547686/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:533324/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:523363/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:518074/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:507003/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:927843/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:384513/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:485773/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:483013/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:479177/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:447829/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:433115/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:414340/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:9916/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:397740/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:773942/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:905170/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:867933/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:840690/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:840190/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:97168/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:824874/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:810911/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:976825/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:782002/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:624208/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:757947/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:988845/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:744531/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:729073/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:702128/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:961177/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:677302/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:649229/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1280889/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1506612/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1468103/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1453722/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1423323/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1373986/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1362819/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1340897/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1338615/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1308938/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1290735/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:367389/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1273449/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1271717/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1173232/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1164153/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1145889/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1139958/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1114071/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1105511/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1037945/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1019013/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1521995/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:378996/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:353358/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:341220/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:33649/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:314481/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:293848/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:270447/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:261573/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:258560/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:232641/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:198389/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:191997/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:167/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1601689/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1559793/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1544684/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1543479/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1540310/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:1538349/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACTTTGCCGTTCAGTTCCAGATGGTCATa  >  1:151092/1‑57 (MQ=255)
        cGCTTTACCATCAACAAACAGCGCGGTCACATTGCCGTTCa                  >  1:1008235/1‑41 (MQ=38)
                                |                                
GCATCAACCGCTTTACCATCAACAAACAGCGCAGTCACTTTGCCGTTCAGTTCCAGATGGTCATA  >  W3110S.gb/2819223‑2819287

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