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 F1 I2 R1 730 35.1 2107516 91.4% 1926269 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,521,934 T→C Q13Q (CAA→CAG)  hofN ← DNA utilization protein HofN

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,521,9340TC100.0% 154.1 / NA 45Q13Q (CAA→CAG) hofNDNA utilization protein HofN
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (22/23);  total (22/23)

TTAGCGTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGTTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAGCGCGATG  >  NC_000913/3521858‑3522008
                                                                            |                                                                          
ttAGCGTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCgctgct                                                                        <  2:674901/81‑1 (MQ=255)
ttAGCGTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGc                                                                         <  1:674902/80‑1 (MQ=255)
  aGCGTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGctgctg                                                                       <  1:674903/80‑1 (MQ=255)
   gCGTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGt                                                                      <  2:674904/80‑1 (MQ=255)
   gCGTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTc                                                                     <  2:674905/81‑1 (MQ=255)
   gCGTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTc                                                                     <  1:674906/81‑1 (MQ=255)
     gTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGc                                                                   >  1:674971/1‑81 (MQ=255)
     gTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGc                                                                   >  1:674960/1‑81 (MQ=255)
     gTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGc                                                                   >  1:674959/1‑81 (MQ=255)
        aTCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCa                                                                 <  1:674907/80‑1 (MQ=255)
           ccaaCGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGc                                                             <  1:674909/78‑1 (MQ=255)
           ccGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAggg                                                              <  2:674908/80‑1 (MQ=255)
             gACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCa                                                            >  2:674973/1‑80 (MQ=255)
             gACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCa                                                            >  2:674955/1‑80 (MQ=255)
              aCGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCaaa                                                          <  1:674910/81‑1 (MQ=255)
              aCGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCaa                                                           >  1:674979/1‑80 (MQ=255)
                 gCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCaaaaaa                                                       >  2:674970/1‑81 (MQ=255)
                 gCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCaaaaaa                                                       >  2:674975/1‑81 (MQ=255)
                  ccAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAaat                                                      <  1:674911/81‑1 (MQ=255)
                      cagcagAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAaattaat                                                  <  1:674912/81‑1 (MQ=255)
                       agcagAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAaattaatt                                                 >  1:674956/1‑81 (MQ=255)
                           gagGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCg                                             >  2:674966/1‑81 (MQ=255)
                            agGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCAAGGGCAAAAAATTAATTGGCgg                                            >  2:674968/1‑81 (MQ=255)
                             ggCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCggg                                           >  1:674996/1‑81 (MQ=255)
                              gcgcAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGt                                          >  2:674981/1‑81 (MQ=255)
                                gcAACGAACATCAGCAACCGGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTtc                                        <  1:674913/81‑1 (MQ=255)
                                gcAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGtt                                         >  1:674967/1‑80 (MQ=255)
                                  aaCGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTtcat                                      <  1:674914/81‑1 (MQ=255)
                                     gAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAg                                   <  2:674915/81‑1 (MQ=255)
                                       aCATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTa                                 <  2:674916/81‑1 (MQ=255)
                                        cATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTAc                                <  2:674917/81‑1 (MQ=255)
                                            aGCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGcc                             <  1:674918/80‑1 (MQ=255)
                                             gCAACCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCtt                           >  1:674984/1‑81 (MQ=255)
                                                aCCAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTcc                         >  1:674964/1‑80 (MQ=255)
                                                  cAGAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCaa                      <  2:674919/81‑1 (MQ=255)
                                                    gAAACGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAgc                    >  2:674963/1‑81 (MQ=255)
                                                     aaaCGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAgcg                   >  2:674962/1‑81 (MQ=255)
                                                     aaaCGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAgcg                   >  2:674969/1‑81 (MQ=255)
                                                       aCGCAGAAAAGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGcc                 <  2:674920/81‑1 (MQ=255)
                                                              aaaGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCa          <  2:674921/81‑1 (MQ=255)
                                                                aGCGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAgc        <  1:674922/81‑1 (MQ=255)
                                                                  cGGTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAgcgc      >  2:674987/1‑81 (MQ=255)
                                                                    gTCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAGCGCGa    >  2:674980/1‑81 (MQ=255)
                                                                     tCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAGCGCGAt   <  2:674924/81‑1 (MQ=255)
                                                                     tCCGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAGCGCGAt   <  2:674923/81‑1 (MQ=255)
                                                                      ccGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAGCGCGATg  >  2:909392/1‑81 (MQ=255)
                                                                       cGGCGCTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAGCGCGATg  <  1:674925/80‑1 (MQ=255)
                                                                            |                                                                          
TTAGCGTTATCCCGACGGCCAGCAGCAGAGGCGCAACGAACATCAGCAACCAGAAACGCAGAAAAGCGGTCCGGCGTTGCTGTCGCCAGGGCAAAAAATTAATTGGCGGGTTCATCAGTACGCCTTCCCAAGCGCCAGCCCCAGCGCGATG  >  NC_000913/3521858‑3522008

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A