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 I3 R1 375 42.1 2927644 71.4% 2090337 57.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 435,436 A→G P193P (CCA→CCG)  thiL → thiamin‑monophosphate kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb435,4360AG86.2% 157.7 / 15.1 65P193P (CCA→CCG) thiLthiamin‑monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base A (1/8);  new base G (0/56);  total (1/64)
Fisher's exact test for biased strand distribution p-value = 1.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.85e-01

ATGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATC  >  W3110S.gb/435393‑435473
                                           |                                     
aTGCTAAAGATGCGTACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAg                     <  1:1664766/62‑1 (MQ=255)
aTGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAg                     <  1:183243/62‑1 (MQ=255)
aTGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAg                     <  1:1170502/62‑1 (MQ=255)
aTGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAg                     <  1:1373374/62‑1 (MQ=255)
aTGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAg                     <  1:412589/62‑1 (MQ=255)
aTGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAg                     <  1:2284921/62‑1 (MQ=255)
aTGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATAGCCGCGTATTTTACAg                     <  1:2000221/62‑1 (MQ=255)
 tGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAg                     <  1:1669556/61‑1 (MQ=255)
  gCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAgg                    >  1:2719737/1‑61 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2713112/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2902938/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2812070/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2730910/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2568813/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:266660/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2639453/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2609385/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2587581/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2584326/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2580046/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2420041/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:290582/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:300097/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:308847/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:35011/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:360457/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:374454/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:411701/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:597269/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:648709/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:667130/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:744131/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:747829/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:790024/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:827242/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:895174/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1888099/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1065387/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1079386/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1107541/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1260380/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:128609/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1347648/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1515322/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1522256/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1602302/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1629347/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1683988/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1773752/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1796875/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1857444/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:1955797/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2007629/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2061937/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2175038/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2197726/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2297072/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2300696/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2348234/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2408950/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:101442/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2422888/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:244317/60‑1 (MQ=255)
                     tGATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:2455477/60‑1 (MQ=255)
                      gATCAAACGTCATCTCCGTCCGTCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATc  <  1:250509/59‑1 (MQ=255)
                                           |                                     
ATGCTAAAGATGCGGACTACTTGATCAAACGTCATCTCCGTCCATCGCCGCGTATTTTACAGGGGCAGGCACTGCGCGATC  >  W3110S.gb/435393‑435473

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