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 F21 I0 R1 57 0.0 661283 90.4% 597799 68.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,788,210 T→A 100% intergenic (+146/‑654) smpB → / → ygaF trans‑translation protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,788,2100TA87.6% 381.0 / 35.3 129intergenic (+146/‑654)smpB/ygaFtrans‑translation protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (16/0);  new base A (56/57);  total (72/57)
Fisher's exact test for biased strand distribution p-value = 5.41e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 130 total aligned reads displayed.

TCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATCTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCTT  >  minE/1788141‑1788270
                                                                     |                                                            
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAt                                                              >  1:272014/1‑70 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:81011/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:304753/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:326890/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:3300/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:4045/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:213883/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:211257/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:526279/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:545878/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:66693/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:129046/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:65896/1‑71 (MQ=255)
tCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATc                                                             >  1:649858/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:442299/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:116746/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:308458/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:333652/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:355653/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:36686/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:376471/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:384922/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:38900/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:655217/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:414905/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:573543/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:647186/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:444420/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:455020/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:470182/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:508161/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:519172/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:647046/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:637111/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:549008/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:55030/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:572825/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:264750/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:223315/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:168396/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:231204/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:220782/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:234117/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:144623/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:242285/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:298334/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:133439/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:199516/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:192948/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:284253/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACtt                                                           >  1:183439/1‑71 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACt                                                            >  1:387789/1‑70 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACt                                                            >  1:197605/1‑70 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACt                                                            >  1:465762/1‑70 (MQ=255)
  acaTCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAAACt                                                            >  1:77127/1‑70 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAGTCTGGTATACTTACCtt  <  1:44415/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:635680/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:169714/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:586721/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:592165/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:596506/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:56143/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:186147/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:618474/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:623991/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:628186/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:633029/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:508378/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:153138/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:149886/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:142352/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:121477/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:67557/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:73860/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:108608/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:218645/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:306179/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:325167/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:277585/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:266456/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:346242/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:364185/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:234457/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:397591/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:436463/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:438104/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:548867/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:211188/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:463863/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:464954/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:47912/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:493166/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:196651/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:509452/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:516001/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:195877/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:191652/70‑1 (MQ=255)
                                                            ggTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCACGGCGCTCATAAATCCGGTATACTTACCtt  <  1:599075/70‑1 (MQ=255)
                                                            ggTACTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:290042/70‑1 (MQ=255)
                                                             gTGCTAAAACTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCtt  <  1:132607/69‑1 (MQ=255)
                                                                     |                                                            
TCACATCCGACACAAATGTTGCCATCCCATTGCTTAATCGAATAAAAATCAGGCTACATGGGTGCTAAATCTTTAACGATAACGCCATTGAGGCTGGTCATGGCGCTCATAAATCTGGTATACTTACCTT  >  minE/1788141‑1788270

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A