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 I1 R1 315 33.5 1889570 98.7% 1865005 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
JC JC NC_000913 2,737,118 IS1 (+) +8 bp intergenic (+235/‑29) bamD → / → raiA outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1978503 =NA (NA)24 (0.750) 21/160 0.6 100% noncoding (768/768 nt) IS1 repeat region
?NC_000913 2737118 = 0 (0.000)intergenic (+235/‑36) bamD/raiA outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor
* ? NC_000913 = 1979270NA (NA)28 (0.880) 23/160 0.4 100% noncoding (1/768 nt) IS1 repeat region
?NC_000913 = 2737125 0 (0.000)intergenic (+242/‑29) bamD/raiA outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor

AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1978581‑1978503
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAATTACTCC  >  NC_000913/2737118‑2737194
                                                                                                                                                            
AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCG                                                                              <  2:210026/80‑1
 AAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAA                                                                            >  1:689104/1‑81
   ATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATT                                                                          >  1:503592/1‑81
   ATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATT                                                                          <  1:689105/81‑1
       GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACC                                                                      <  2:361536/81‑1
          GAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAG                                                                   <  2:361554/81‑1
             CTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACG                                                                <  2:4129/81‑1
              TGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGG                                                               >  2:503590/1‑81
                CATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGA                                                             <  2:4116/81‑1
                                GGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAAT                                             <  1:56282/81‑1
                                   ATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTA                                          >  1:503591/1‑81
                                      ATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGA                                       >  1:503600/1‑81
                                           AACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATG                                  <  1:60778/81‑1
                                           AACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAA                                    <  1:209970/79‑1
                                            ACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGA                                 <  1:4130/81‑1
                                            ACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGA                                 <  2:60777/81‑1
                                            ACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGA                                 <  2:4123/81‑1
                                            ACATAAAACACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATG                                  >  2:503594/1‑80
                                                    CACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACC                         <  2:4107/81‑1
                                                     ACTATCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTAC                          >  1:503606/1‑79
                                                         TCAATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAA                    <  1:689068/81‑1
                                                            ATAAGTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAAC                  >  1:503596/1‑80
                                                                GTTGGAGTCATTACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATG             <  2:689071/81‑1
                                                                            ACCGAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAATTACTCC  <  2:503572/80‑1
                                                                                                                                                            
AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1978581‑1978503
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAATTCACCAAGACGGGAAGACAAGAGGTAAAATTTATGACAATGAACATTACCAGCAAACAAATGGAAATTACTCC  >  NC_000913/2737118‑2737194

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A