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 F2 I228 R1 214 26.5 1448192 97.1% 1406194 86.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,934,995 +C intergenic (‑308/‑173) yieP ← / → BW25113_RS19520 FadR/GntR family transcriptional regulator/16S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,934,9911.C100.0% 97.1 / NA 33intergenic (‑304/‑177)yieP/BW25113_RS19520FadR/GntR family transcriptional regulator/16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (17/16);  total (17/16)

GGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGA  >  NZ_CP009273/3934915‑3935074
                                                                             |                                                                                   
ggggTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCt                                                                         <  2:34031/90‑1 (MQ=255)
           gagaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagca                                                              >  2:684052/1‑90 (MQ=255)
           gagaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagca                                                              >  2:250031/1‑90 (MQ=255)
           gagaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagca                                                              >  1:618527/1‑90 (MQ=255)
           gagaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTAAGAAaaagta                                                              >  1:19903/1‑88 (MQ=11)
                cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCg                                                         >  1:252983/1‑90 (MQ=255)
                  ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc                                                       >  2:249241/1‑90 (MQ=255)
                  ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc                                                       >  1:102306/1‑90 (MQ=255)
                  ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc                                                       >  1:87298/1‑90 (MQ=255)
                     gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt                                                    <  1:353154/90‑1 (MQ=255)
                             aGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTa                                            <  2:614121/90‑1 (MQ=255)
                             aGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTa                                            <  1:189741/90‑1 (MQ=255)
                                 aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGTGGCACTGCTCTTTAACaa                                        <  2:165946/90‑1 (MQ=14)
                                       aatGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATc                                  <  1:505215/90‑1 (MQ=255)
                                       aatGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATc                                  <  1:612842/90‑1 (MQ=255)
                                        atGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCa                                 >  1:174262/1‑90 (MQ=255)
                                         tGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCGCTGCTCTTTAACAATTTATCAg                                <  2:379381/90‑1 (MQ=11)
                                         tGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAg                                <  2:618527/90‑1 (MQ=255)
                                             tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc                                                  <  2:138654/68‑1 (MQ=255)
                                             tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc                                                  >  1:138654/1‑68 (MQ=255)
                                             tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa                            >  2:335441/1‑90 (MQ=255)
                                                    gTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCtgtgt                     >  2:214236/1‑90 (MQ=255)
                                                         gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa                >  2:341164/1‑90 (MQ=255)
                                                            aaaGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt                                                    <  1:430642/51‑1 (MQ=14)
                                                            aaaGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt                                                    >  2:430642/1‑51 (MQ=14)
                                                            aaaGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTa                                            >  1:680662/1‑59 (MQ=14)
                                                            aaaGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTa                                            <  2:680662/59‑1 (MQ=14)
                                                            aaaGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTc             >  2:179343/1‑90 (MQ=255)
                                                            aaaGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTc             <  1:217336/90‑1 (MQ=255)
                                                              aGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGa           <  2:447454/90‑1 (MQ=255)
                                                                     tatGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACg    <  1:304973/90‑1 (MQ=255)
                                                                      atGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACgg   >  2:395353/1‑90 (MQ=255)
                                                                       tGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGa  <  1:179343/90‑1 (MQ=255)
                                                                             |                                                                                   
GGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGA  >  NZ_CP009273/3934915‑3935074

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTC  >  NZ_CP009273/3934916‑3935085
                                                                                |                                                                                          
GGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCA                                                                         >  SRR3722112.628070/1‑100 (MQ=9)
GGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTAAGAAAAAGTA                                                                         >  SRR3722112.20152/1‑100 (MQ=6)
     CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCG                                                                    >  SRR3722112.255971/1‑100 (MQ=24)
       CCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGC                                                                  >  SRR3722112.103578/1‑100 (MQ=24)
       CCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGC                                                                  >  SRR3722112.88381/1‑100 (MQ=24)
                    cggcagcgtcagatgtgtataagagacagCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAC                                                     <  SRR3722112.436483/71‑1 (MQ=27)
                    GCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAC                                                     <  SRR3722112.357635/100‑1 (MQ=24)
                            AGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATC                                             <  SRR3722112.192066/100‑1 (MQ=24)
                             GCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCA                                            >  SRR3722112.176393/1‑100 (MQ=24)
                                  AATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAActgtctcttata                                       >  SRR3722112.140386/1‑88 (MQ=25)
                                      AATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTG                                   <  SRR3722112.512565/100‑1 (MQ=24)
                                      AATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTG                                   <  SRR3722112.622258/100‑1 (MQ=24)
                                        cggcagcgtcagatgtgtataagagacagatgcacacCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTG                                 <  SRR3722112.730933/63‑1 (MQ=10)
                                                 CTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCctgtctcttatacacatctga                        >  SRR3722112.691306/1‑79 (MQ=26)
                                                           AAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGG              <  SRR3722112.219953/100‑1 (MQ=19)
                                                             cagGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT            <  SRR3722112.554964/97‑1 (MQ=6)
                                                                  ATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATctgtctcttat       >  SRR3722112.356757/1‑89 (MQ=7)
                                                                    TATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAAC     <  SRR3722112.308476/100‑1 (MQ=6)
                                                                     ATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGctgtctcttatacacatctgacgctgccg    >  SRR3722112.102679/1‑71 (MQ=8)
                                                                     ATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACG    >  SRR3722112.570724/1‑100 (MQ=6)
                                                                      TGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGT   <  SRR3722112.181537/100‑1 (MQ=6)
                                                                       GCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGctgtctcttatacacatctgacgctgccgac  >  SRR3722112.415356/1‑69 (MQ=8)
                                                                       GCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTC  >  SRR3722112.604821/1‑100 (MQ=6)
                                                                       GCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTC  >  SRR3722112.693647/1‑100 (MQ=6)
                                                                                |                                                                                          
GGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTC  >  NZ_CP009273/3934916‑3935085

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑