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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,474,827 G→T 25.8% intergenic (+125/‑109) nrdA → / → nrdB ribonucleoside diphosphate reductase 1, alpha subunit/ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,474,8270GT25.8% 72.0 / 13.2 31intergenic (+125/‑109)nrdA/nrdBribonucleoside diphosphate reductase 1, alpha subunit/ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like
Reads supporting (aligned to +/- strand):  ref base G (18/5);  new base T (6/2);  total (24/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.14e-01

GCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGCGTAA  >  minE/1474772‑1474895
                                                       |                                                                     
gcgcCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑tt                                                       <  1:3803575/71‑1 (MQ=255)
    cAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTg                                                     >  1:5391049/1‑69 (MQ=255)
           gCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGa                                            <  1:5172349/71‑1 (MQ=255)
               cAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGAt                                           >  1:4350047/1‑68 (MQ=255)
                aGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAc                                                                  >  1:106070/1‑45 (MQ=255)
                aGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGa                                       >  1:1587807/1‑71 (MQ=255)
                      cGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACgcgc                                  >  1:2051645/1‑70 (MQ=255)
                        tgTGCTGGACGTAGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcgcgg                                  >  1:1857138/2‑68 (MQ=2)
                        tgTGCTGGACGTAGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcgcgg                                  >  1:4615802/2‑68 (MQ=2)
                         gTGCTGGACGTAGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcgcggt                                 <  1:2532356/69‑3 (MQ=2)
                               gATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa                        >  1:77001/1‑71 (MQ=255)
                               gATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa                        >  1:5542865/1‑71 (MQ=255)
                                aTGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCAt                       >  1:661098/1‑71 (MQ=255)
                                   cAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAg                    >  1:2206749/1‑71 (MQ=255)
                                    aGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑tt                                                       >  1:922637/1‑35 (MQ=255)
                                    aGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑tt                                                       >  1:5494721/1‑35 (MQ=255)
                                    aGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCAt                       >  1:5051680/1‑68 (MQ=2)
                                        taaaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTc                           >  1:3925360/3‑60 (MQ=2)
                                        taaaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCATCAGGcat                <  1:5142320/69‑2 (MQ=2)
                                         gAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAg              >  1:5173600/1‑71 (MQ=255)
                                          aaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGa                                       >  1:431275/1‑46 (MQ=9)
                                          aaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcgcg                                   >  1:4923270/1‑50 (MQ=9)
                                             gCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATg          >  1:1205345/1‑71 (MQ=255)
                                              ccTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgc         >  1:5169314/1‑71 (MQ=255)
                                               cTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcg        <  1:2114059/71‑1 (MQ=255)
                                                 tATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCg                             <  1:2806915/48‑1 (MQ=255)
                                                  aTCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACgcgc                                  >  1:5502626/1‑42 (MQ=255)
                                                  aTCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCAt                       >  1:862763/1‑53 (MQ=255)
                                                  aTCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcggcg     >  1:4687063/1‑71 (MQ=255)
                                                  aTCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcggcg     >  1:302316/1‑71 (MQ=255)
                                                     cGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGCGTaa  <  1:445863/71‑1 (MQ=255)
                                                       |                                                                     
GCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGCGTAA  >  minE/1474772‑1474895

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