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
A3 F1 I1 R1 502 34.8 1912488 98.2% 1878063 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,599,709 (T)5→6 intergenic (‑51/+220) livJ ← / ← rpoH branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,599,7041.T100.0% 58.9 / NA 17intergenic (‑46/+225)livJ/rpoHbranched chain amino acid/phenylalanine ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (7/10);  total (7/10)

CATCCTGCCAGTAACGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTG‑TTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTAGCAGCATACTCTGCTAAAACA  >  NC_000913/3599624‑3599771
                                                                                 |                                                                   
cATCCTGCCAGTAACGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGAtgttg                                                                      >  2:686286/1‑81 (MQ=255)
 aTCCTGCCAGTAACGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGAtgttg‑t                                                                    >  1:686278/1‑81 (MQ=255)
    cTGCCAGTAACGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTG‑tttt                                                                 <  1:686251/81‑1 (MQ=255)
    cTGCCAGTAACGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTG‑ttt                                                                  <  1:686252/80‑1 (MQ=255)
         aGTAACGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTG‑ttttttcag                                                            <  2:686253/81‑5 (MQ=255)
            aaCGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCAc                                                          >  1:686288/1‑81 (MQ=255)
              cGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACtt                                                        >  1:686304/1‑81 (MQ=255)
              cGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACtt                                                        <  2:686254/81‑1 (MQ=255)
                  ttACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACTTTAtt                                                    >  1:686297/1‑81 (MQ=255)
                   tACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACTTTAtt                                                    <  1:686255/80‑1 (MQ=255)
                              ttCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCa                                        <  2:686256/81‑1 (MQ=255)
                                   ccTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGAc                                    >  1:686287/1‑80 (MQ=255)
                                    cTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACt                                   <  1:686257/80‑1 (MQ=255)
                                    cTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTa                                  >  1:686295/1‑81 (MQ=255)
                                             cccATTCTTCTGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCtt                         >  2:686289/1‑81 (MQ=255)
                                                   cttctGGTTATTACGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTagca                    <  1:686258/80‑1 (MQ=255)
                                                          ttattaCGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTAGCAGCATActc            <  1:686259/81‑1 (MQ=255)
                                                            attaCGTTGGTTGTGATGGTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTAGCAGCATActct           <  1:686261/80‑1 (MQ=255)
                                                            attaCGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTAGCAGCATActct           <  1:686260/80‑1 (MQ=255)
                                                               aCGTGTGTTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTAGCAGCATACTCTGCt        <  2:686262/80‑1 (MQ=255)
                                                                  tgtgtTGTGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTAGCAGCATACTCTGCTaaaa    >  2:686294/1‑81 (MQ=255)
                                                                    tgttgtGATGTTGTTTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTAGCAGCATACTCTGCTAAAACa  <  1:686263/81‑1 (MQ=255)
                                                                                 |                                                                   
CATCCTGCCAGTAACGCTTTACCCTTTATGTTCATCCTGAGAATCCCCATTCTTCTGGTTATTACGTGTGTTGTGATGTTG‑TTTTTCAGCACTTTATTTCGTTTTATGCATGACTACCCGTGCTTTAGCAGCATACTCTGCTAAAACA  >  NC_000913/3599624‑3599771

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A