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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,328,372 G→A 51.5% F131F (TTC→TTT)  wzxC ← colanic acid exporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,328,3720GA51.5% ‑5.5 / 47.9 33F131F (TTC→TTT) wzxCcolanic acid exporter
Reads supporting (aligned to +/- strand):  ref base G (9/7);  new base A (7/10);  total (16/17)
Fisher's exact test for biased strand distribution p-value = 4.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01

CGCCAGCACCGCGCTGGTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCCAG  >  minE/1328303‑1328434
                                                                     |                                                              
cGCCAGCACCGCGCTGGTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCgg                                                                >  1:4042473/1‑70 (MQ=255)
        ccGCGCTGGTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGc                                                       <  1:2737104/71‑1 (MQ=255)
              tGGTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTgg                                                 >  1:3439053/1‑71 (MQ=255)
                gTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGCCCGTgggg                                               <  1:163527/71‑1 (MQ=255)
                gTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGCCCGTgggg                                               <  1:168379/71‑1 (MQ=255)
                gTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGCCCGTgggg                                               <  1:4185374/71‑1 (MQ=255)
                gTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGCCCGTgggg                                               <  1:3757848/71‑1 (MQ=255)
                gTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGCCCGTgggg                                               <  1:2437950/71‑1 (MQ=255)
                        cATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGCCCGTgggg                                               <  1:3429975/63‑1 (MQ=255)
                          tGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTACcaca                                     <  1:3797141/71‑1 (MQ=255)
                               aTTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGaaa                                                              >  1:2934278/1‑41 (MQ=255)
                               aTTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGaaa                                                              >  1:755520/1‑41 (MQ=255)
                               aTTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGaaa                                                              >  1:3868013/1‑41 (MQ=255)
                               aTTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGaaa                                                              >  1:2662059/1‑41 (MQ=255)
                               aTTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGaaa                                                              >  1:3471751/1‑41 (MQ=255)
                                 tttGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGATGCCCGTg                                                  <  1:1357688/51‑1 (MQ=255)
                                   tgttgAACTCCAGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGTTTACCACAAACGCCAGc                            >  1:2880835/1‑71 (MQ=255)
                                    gttgAACTCCAGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTTCCACAAACGCCAGc                            >  1:1650419/1‑70 (MQ=255)
                                     ttgAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGCCCGTg                                                  <  1:1741316/47‑1 (MQ=255)
                                       gAACTCCAGCTCTTTTTGCATCAACGCGCGAAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGa                          >  1:1771662/1‑69 (MQ=255)
                                           tCCAGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACg                                 <  1:2033165/58‑1 (MQ=255)
                                             cAGCTCTTTTTGCATCAACGCGCGGAACTGTT‑CCCGTGGGGGATTACCACAAACGCCAGCGATAATGttt                  >  1:36640/1‑70 (MQ=255)
                                              aGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGtttt                 <  1:2700678/71‑1 (MQ=255)
                                              aGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGtttt                 <  1:2526774/71‑1 (MQ=255)
                                              aGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGtttt                 <  1:1926084/71‑1 (MQ=255)
                                                  ctTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAAt              >  1:3154763/1‑70 (MQ=255)
                                                     tttGCATCAACGCGCGAAACTGTTGCCCGTGGGGGATTACCACaaa                                   >  1:4030783/1‑46 (MQ=255)
                                                     tttGCATCAACGCGCGAAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATc             <  1:728929/68‑1 (MQ=255)
                                                     tttGCATCAACGCGCGAAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAAc          >  1:3635553/1‑71 (MQ=255)
                                                            cAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGc     >  1:49710/1‑69 (MQ=255)
                                                            cAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGc     >  1:2263071/1‑69 (MQ=255)
                                                            cAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGc     >  1:1750002/1‑69 (MQ=255)
                                                             aaCGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCCAg  <  1:3754392/71‑1 (MQ=255)
                                                             aaCGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCAAg  >  1:1489077/1‑71 (MQ=255)
                                                             aaCGCGCGAAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCCAg  >  1:3249070/1‑71 (MQ=255)
                                                             aaCGCGCGAAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCCAg  >  1:2566121/1‑71 (MQ=255)
                                                             aaCGCGCGAAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCCAg  >  1:1660595/1‑71 (MQ=255)
                                                             aaCGCGCCAAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCCAg  >  1:1863390/1‑71 (MQ=255)
                                                              aCGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCCAg  <  1:2782793/70‑1 (MQ=255)
                                                                     |                                                              
CGCCAGCACCGCGCTGGTTTCGATCATGCCGATTTTGTTGAACTCCAGCTCTTTTTGCATCAACGCGCGGAACTGTTGCCCGTGGGGGATTACCACAAACGCCAGCGATAATGTTTTAATCAACGGTGCCAG  >  minE/1328303‑1328434

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