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
A5 F28 I2 R1 721 0.0 1472758 54.8% 807071 56.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,854,178 T→G V395V (GTT→GTG)  fhlA → DNA‑binding transcriptional activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,854,1780TG97.3% 315.1 / ‑1.6 112V395V (GTT→GTG) fhlADNA‑binding transcriptional activator
Reads supporting (aligned to +/- strand):  ref base T (0/3);  new base G (109/0);  total (109/3)
Fisher's exact test for biased strand distribution p-value = 4.39e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

Only 100 of 112 total aligned reads displayed.

CAGCGTGCTTAAACAAGTTGAAATGGTGGCGCAAAGTGACAGTACCGTGCTGATCCTCGGTGAAACTGG  >  W3110S.gb/2854160‑2854228
                  |                                                  
cAGCGTGCTTAAACAAGTTGAAATGGTGGCGCAAAGTGACAGTACCGTGCTGATCCTCGGTg         <  1:989118/62‑1 (MQ=255)
cAGCGTGCTTAAACAAGTTGAAATGGTGGCGCAAAGTGACAGTACCGTGCTGATCCTCGGTg         <  1:1448056/62‑1 (MQ=255)
cAGCGTGCTTAAACAAGTTGAAATGGTGGCGCAAAGTGACAGTACCGTGCTGATCCTCGGTg         <  1:43842/62‑1 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTAcc                         >  1:684017/1‑39 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTc             >  1:715313/1‑51 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGTAACTgg  >  1:1278245/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:563430/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:312938/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:559554/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:552249/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:540130/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:524821/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:518772/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:50834/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:504625/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:503503/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:462673/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:311411/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:454735/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:448653/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:307516/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:431906/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:422596/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:390863/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:37486/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:347018/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:342915/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:314699/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:767218/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:974920/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:907795/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:887060/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:859520/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:856762/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:838151/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:825433/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:79971/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:791552/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:786892/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:784348/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:574892/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:752008/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:709612/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:690767/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:680858/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:673332/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:672718/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:669851/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:653741/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:651642/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:63529/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1137928/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:308556/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1249776/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1240076/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1236726/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1217010/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1207505/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:119746/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1183702/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1163076/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1159834/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1151584/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1326338/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1128005/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1112243/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1104464/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1091885/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1084599/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1083239/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1078304/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1058046/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1054049/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1038311/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1036338/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1446178/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1031363/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:298975/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:289050/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:28860/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:262596/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:235522/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:214274/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:21309/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:193373/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:191076/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1464205/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1342223/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1435477/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1415010/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1386672/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1371650/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1370907/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1368978/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:13675/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1353512/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTgg  >  1:1344591/1‑62 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTg   >  1:201159/1‑61 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTg   >  1:1255022/1‑61 (MQ=255)
       cTTAAACAAGTGGAAATGGTGGCGCAAAGTGACAGTACCGTTCTGATCCTCGGTGAAACTg   >  1:1296996/1‑61 (MQ=255)
                  |                                                  
CAGCGTGCTTAAACAAGTTGAAATGGTGGCGCAAAGTGACAGTACCGTGCTGATCCTCGGTGAAACTGG  >  W3110S.gb/2854160‑2854228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A