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 F1 I2 R1 77 34.8 1608548 95.0% 1528120 114.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,271,600 (C)5→6 coding (171/1146 nt) garK ← glycerate kinase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,271,5951.C94.7% 63.2 / ‑2.7 19coding (176/1146 nt)garKglycerate kinase I
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (10/8);  total (11/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01

CAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AG‑CCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCGCTG  >  NC_000913/3271483‑3271723
                                                                                                                  |                                                                                                                                
cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑Ag                                                                                                                                   <  1:786099/113‑1 (MQ=255)
cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑Ag                                                                                                                                   >  2:786099/1‑113 (MQ=255)
                              cgcgGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAAc                                                                           >  1:428312/1‑139 (MQ=255)
                              cgcgGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAAc                                                                           >  1:149130/1‑139 (MQ=255)
                              cgcgGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAAc                                                                           >  1:535158/1‑139 (MQ=255)
                                   ttttGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa                                                                      >  2:245502/1‑139 (MQ=255)
                                   ttttGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa                                                                      <  2:408499/139‑1 (MQ=255)
                                     ttGCCATCGCCGGAGATCCCCCAGCTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGGGGCTGCAATCATCGCTTCCACCGTGCCTTCGCCACCGTCGGCAACCGGAACa                                                                    <  1:512543/139‑1 (MQ=255)
                                                  agaTCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACtg                                                         >  1:738359/1‑137 (MQ=255)
                                                  agaTCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACtg                                                         <  2:738359/137‑1 (MQ=255)
                                                       ccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAatc                                                                                                              >  2:546246/1‑79 (MQ=255)
                                                       ccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AG‑cccccctgg                                                                                                                         <  1:383294/67‑5 (MQ=255)
                                                       ccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AG‑cccccctgg                                                                                                                         >  2:383294/1‑63 (MQ=255)
                                                       ccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AG‑c                                                                                                                                 >  1:672939/1‑59 (MQ=255)
                                                       ccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AG‑c                                                                                                                                 <  2:672939/59‑1 (MQ=255)
                                                       ccccAACTGGCATACACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAatc                                                                                                              <  1:546246/79‑1 (MQ=255)
                                                                   ttCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTcc                                      >  1:585795/1‑139 (MQ=255)
                                                                      aCTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGa                                   <  2:585795/139‑1 (MQ=255)
                                                                               cccAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCAcc                                                                                                  >  2:410011/1‑67 (MQ=255)
                                                                               cccAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCAcc                                                                                                  <  1:410011/67‑1 (MQ=255)
                                                                                  aGCGGCCCTGTAACCCAGGCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCt                       <  2:662674/139‑1 (MQ=255)
                                                                                                   ggCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTc      >  1:478049/1‑139 (MQ=255)
                                                                                                    gCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAatca                                                                                                             <  2:563651/35‑1 (MQ=255)
                                                                                                    gCGTGACGTTC‑AGCCCCCCTGGGTGGCTGCAatca                                                                                                             >  1:563651/1‑35 (MQ=255)
                                                                                                       tGACGTTCAAC‑CCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCGCTg  >  2:775721/1‑139 (MQ=255)
                                                                                                                  |                                                                                                                                
CAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTC‑AG‑CCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCGCTG  >  NC_000913/3271483‑3271723

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A