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 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,855,731 G→T 23.3% intergenic (‑269/‑18) ygbA ← / → mutS hypothetical protein/methyl‑directed mismatch repair protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,855,7310GT23.3% 76.1 / 9.2 30intergenic (‑269/‑18)ygbA/mutShypothetical protein/methyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base G (12/11);  new base T (4/3);  total (16/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.23e-01

CTCCGGTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATG  >  W3110S.gb/2855662‑2855790
                                                                     |                                                           
cTCCGGTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAggg                                                            <  1:140837/71‑1 (MQ=255)
      tATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCgg                                                      <  1:2781456/71‑1 (MQ=255)
      tATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCg                                                       >  1:3890201/1‑70 (MQ=255)
          aTGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACa                                                   >  1:1950529/1‑70 (MQ=255)
          aTGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACa                                                   >  1:4139530/1‑70 (MQ=255)
          aTGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACAt                                                  <  1:2017205/71‑1 (MQ=255)
             tgCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATaa                                                <  1:488559/70‑1 (MQ=255)
                   ttATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCAt                                          >  1:2141176/1‑70 (MQ=255)
                      tgtgATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGa                                                     <  1:4083592/56‑1 (MQ=255)
                           ttACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATaa                                                >  1:59231/1‑56 (MQ=255)
                           ttACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCaa                                  >  1:998240/1‑70 (MQ=255)
                                 cGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGaaaa                           >  1:2132749/1‑71 (MQ=255)
                                  gAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAAt                          >  1:1297512/1‑71 (MQ=255)
                                      aTAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCAt                                          <  1:732696/51‑1 (MQ=255)
                                      aTAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTc                       >  1:314423/1‑70 (MQ=255)
                                         aaaaCCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGac                    <  1:1433666/70‑1 (MQ=255)
                                           aaCCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATg                                         <  1:823573/47‑1 (MQ=255)
                                             ccATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCCacgccca               <  1:1666740/71‑1 (MQ=255)
                                                tCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcccatac            >  1:4036708/1‑71 (MQ=255)
                                                 cacaCCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcccatacg           >  1:1058097/1‑71 (MQ=255)
                                                   cacCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcccatacgcc         <  1:45715/71‑1 (MQ=255)
                                                      cccATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgcccatacgcccat      >  1:1134987/1‑71 (MQ=255)
                                                       taattTAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgggcagggggc      >  1:779844‑M1/3‑31 (MQ=255)
                                                        aatTTAATATCAGTAAGCCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgggcag           >  1:842587‑M1/2‑30 (MQ=255)
                                                        aatTTAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgggcag           >  1:2185561‑M1/2‑30 (MQ=255)
                                                         aTTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgccca               <  1:3265051/59‑1 (MQ=255)
                                                         aTTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGacgc                  <  1:2156569/56‑1 (MQ=255)
                                                          tttAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgggcagggggcaagt  <  1:2498356‑M1/71‑44 (MQ=255)
                                                          tttAATATCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaa                   >  1:2976159‑M1/1‑28 (MQ=255)
                                                          tttAATATCAGTAAACCGGACATAACCCatgaagaaaaat                                 <  1:3009564‑M1/40‑13 (MQ=255)
                                                               tatCAGTAAACCGGACATAACCCatgaagaaaaatcgcgcttttttgaagtgg               <  1:2862287‑M1/53‑31 (MQ=255)
                                                                     |                                                           
CTCCGGTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATG  >  W3110S.gb/2855662‑2855790

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