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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 712,019 G→A 13.5% intergenic (‑132/+8) fldA ← / ← ybfE flavodoxin 1/LexA regulated protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb712,0190GA13.5% 244.0 / 25.0 89intergenic (‑132/+8)fldA/ybfEflavodoxin 1/LexA regulated protein
Reads supporting (aligned to +/- strand):  ref base G (48/29);  new base A (9/3);  total (57/32)
Fisher's exact test for biased strand distribution p-value = 5.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

AATCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTC  >  W3110S.gb/711950‑712089
                                                                     |                                                                      
aaTCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGt                                                                       >  1:427938/1‑71 (MQ=255)
aaTCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGt                                                                       >  1:3822656/1‑71 (MQ=255)
aaTCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGt                                                                       >  1:2055893/1‑71 (MQ=255)
aaTCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGt                                                                       >  1:1945657/1‑71 (MQ=255)
    aTAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGa                                                                    <  1:130661/70‑1 (MQ=255)
             cAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           >  1:345/1‑70 (MQ=255)
                 cAGTCTTGCGGAATCAGCAAACGAGCAGGACTGAACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           <  1:425265/66‑1 (MQ=255)
                     cTTGCGGAATCAGCAAACGAGCAGGACTGCCCACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCt                                                   >  1:2340916/1‑70 (MQ=255)
                     cTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCt                                                   >  1:1122958/1‑70 (MQ=255)
                     cTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCt                                                   >  1:2320142/1‑70 (MQ=255)
                      ttGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGa                                                 >  1:4064337/1‑71 (MQ=255)
                      ttGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGa                                                 >  1:2962020/1‑71 (MQ=255)
                      ttGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGa                                                 >  1:1720869/1‑71 (MQ=255)
                            aaTCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           <  1:1007968/55‑1 (MQ=255)
                            aaTCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           <  1:2545510/55‑1 (MQ=255)
                            aaTCAGCAAACGAGCAGGACTGCACACTGTGCTACATCAAAGTGGAAATTTAAAc                                                           <  1:1073594/55‑1 (MQ=255)
                                aGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           <  1:678204/51‑1 (MQ=255)
                                aGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           <  1:3860755/51‑1 (MQ=255)
                                aGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           <  1:2029511/51‑1 (MQ=255)
                                aGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAAGGATGCCCTGa                                                 >  1:1312829/1‑61 (MQ=255)
                                aGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAgcg                                       >  1:2826535/1‑71 (MQ=255)
                                aGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAgcg                                       >  1:4032789/1‑71 (MQ=255)
                                aGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAgcg                                       >  1:2069846/1‑71 (MQ=255)
                                  cAAACGAGCAGGACTGCACACTGTGCTACATGAAAATGGAAATTTAAACGa                                                         >  1:1497118/1‑51 (MQ=255)
                                  cAAACGAGCAGGACTGCACACTGTGCTACATGAAAATGGAAATTTAAACGa                                                         >  1:2228720/1‑51 (MQ=255)
                                  cAAACGAGCAGGACTGCACACTGTGCTACATGAAAATGGAAATTTAAACGa                                                         >  1:2013219/1‑51 (MQ=255)
                                  cAAACGAGCAGGACTGCACACTGTGCTACATGAAAATGGAAATTTAAACGa                                                         >  1:4003359/1‑51 (MQ=255)
                                  cAAACGAGCAGGACTGCACACTGTGCTACATGAAAATGGAAATTTAAACGa                                                         >  1:625150/1‑51 (MQ=255)
                                   aaaCGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGa                                                         >  1:769418/1‑50 (MQ=255)
                                   aaaCGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATATAAACGa                                                         >  1:234427/1‑50 (MQ=255)
                                   aaaCGAGCAGGACTGCACACTGTGCTACATGAAAATGGAAATTTAAACGATGCCCTGACTACGCAGcgccg                                    >  1:2300083/1‑71 (MQ=255)
                                       gAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAg                                <  1:3130819/71‑1 (MQ=255)
                                       gAGCAGGACTGCACACTGTGCTACATGAAAATGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAg                                >  1:1050948/1‑71 (MQ=255)
                                         gCAGGACTGAACACTGTGCTACATGAAAATGGAAATTTAAAc                                                           <  1:3560551/42‑1 (MQ=38)
                                             gACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgctg                          <  1:1107388/71‑1 (MQ=255)
                                             gACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgctg                          <  1:2959504/71‑1 (MQ=255)
                                              aCTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgctg                          <  1:1865321/70‑1 (MQ=255)
                                              aCTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgctg                          >  1:1373750/1‑70 (MQ=255)
                                              aCTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgctg                          >  1:2682189/1‑70 (MQ=255)
                                              aCTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgctg                          >  1:2925060/1‑70 (MQ=255)
                                               cTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAg                                >  1:459380/1‑63 (MQ=255)
                                               cTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAg                                >  1:454453/1‑63 (MQ=255)
                                               cTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCa                        >  1:3804102/1‑71 (MQ=255)
                                               cTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCa                        >  1:1051207/1‑71 (MQ=255)
                                                tGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           <  1:1101501/35‑1 (MQ=255)
                                                tGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                           <  1:1339584/35‑1 (MQ=255)
                                                tGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGc                                           <  1:1419033/51‑1 (MQ=255)
                                                tGCACACTGTGCTACATGAAAATGGAAATTTAAAc                                                           <  1:804239/35‑1 (MQ=255)
                                                 gCACACTGTGCTACATGAAAATGGAAATTTAAACGATGCCCTGACTACGCAgcgc                                      >  1:1361836/1‑55 (MQ=255)
                                                 gCACACTGTGCTACATGAAAATGGAAATTTAAACGATGCCCTGACTACGCAgcgc                                      >  1:3131324/1‑55 (MQ=255)
                                                  cacaCTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAtt                      >  1:3819727/1‑70 (MQ=255)
                                                  cacaCTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAtt                      >  1:3491659/1‑70 (MQ=255)
                                                  cacaCTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAtt                      >  1:3891741/1‑70 (MQ=255)
                                                  cacaCTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAtt                      >  1:3000496/1‑70 (MQ=255)
                                                  cacaCTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAtt                      >  1:1729204/1‑70 (MQ=255)
                                                  cacaCTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAtt                      >  1:2976009/1‑70 (MQ=255)
                                                  cacaCTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAtt                      >  1:2606526/1‑70 (MQ=255)
                                                  cacaCTGTGCTACATGAAAATGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAtt                      <  1:3490078/70‑1 (MQ=255)
                                                   acacTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTaa                    <  1:1004470/71‑1 (MQ=255)
                                                    cacTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGa                                                 >  1:3169873/1‑41 (MQ=255)
                                                    cacTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGa                                                 >  1:3016565/1‑41 (MQ=255)
                                                    cacTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAAc                   <  1:4075792/71‑1 (MQ=255)
                                                      cTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACAt                 >  1:3639471/1‑71 (MQ=255)
                                                       tgtgCTACATGAAAGTGGAAATTTAAACGATGCCCt                                                   <  1:2265504/36‑1 (MQ=255)
                                                       tgtgCTACATGAAAGTGGAAATTTAAACGATGCCCt                                                   <  1:881562/36‑1 (MQ=255)
                                                       tgtgCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACAtc                >  1:988611/1‑71 (MQ=255)
                                                        gtgCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACAtct               >  1:3568737/1‑71 (MQ=255)
                                                        gtgCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACAtct               >  1:3731840/1‑71 (MQ=255)
                                                        gagCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACAtct               >  1:2986031/3‑71 (MQ=255)
                                                         tgCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTaa                    >  1:3977872/1‑65 (MQ=255)
                                                         tgCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTaa                    >  1:2274232/1‑65 (MQ=255)
                                                         tgCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGAAGCGCCGCCAGTTGCTGCATTaa                    >  1:1085348/1‑65 (MQ=255)
                                                           cTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATctct             <  1:1259508/70‑1 (MQ=255)
                                                            tACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCgccgcc                                  <  1:342261/48‑1 (MQ=255)
                                                            tACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCgccgcc                                  <  1:3098906/48‑1 (MQ=255)
                                                            tACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgc                            <  1:1667310/54‑1 (MQ=255)
                                                              cATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCg          >  1:866969/1‑70 (MQ=255)
                                                              cATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGa         >  1:2143018/1‑71 (MQ=255)
                                                              cATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGa         >  1:467362/1‑71 (MQ=255)
                                                               aTGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGAt        <  1:272125/71‑1 (MQ=255)
                                                                tGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCg          <  1:2155212/68‑1 (MQ=255)
                                                                tGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCg          <  1:4000926/68‑1 (MQ=255)
                                                                  aaaGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGAt        >  1:3031740/1‑68 (MQ=255)
                                                                  aaaGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGAt        >  1:2379994/1‑68 (MQ=255)
                                                                  aaaGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCa      <  1:4084905/70‑1 (MQ=255)
                                                                  aaaGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCa      <  1:2838742/70‑1 (MQ=255)
                                                                   aaGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGt    >  1:3134269/1‑71 (MQ=255)
                                                                   aaGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGt    <  1:837839/71‑1 (MQ=255)
                                                                   aaGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGt    >  1:3224601/1‑71 (MQ=255)
                                                                     gTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTc  >  1:1600499/1‑71 (MQ=255)
                                                                     |                                                                      
AATCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTC  >  W3110S.gb/711950‑712089

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