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
A9 F59 I1 R1 22 41.8 1821698 89.9% 1637706 142.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
JC JC NC_000913 1,293,032 IS1 (–) +8 bp intergenic (‑110/‑488) hns ← / → tdk DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 257908 =NA (NA)45 (0.900) 38/284 0.3 100% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 1293039 0 (0.000)intergenic (‑117/‑488) hns/tdk DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase
* ? NC_000913 1293032 =0 (0.000)59 (1.180) 46/284 0.1 100% intergenic (‑110/‑495) hns/tdk DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase
?NC_000913 = 1979270 NA (NA)noncoding (1/768 nt) IS1 repeat region

CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/258048‑257908
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAAT  <  NC_000913/1293039‑1292903
                                                                                                                                                                                                                                                                                      
CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCG                                                                                                                                         >  2:694181/1‑143
CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGACATCATCAGAACATAAAACACAATCAATAAGCAGGAGACATTAACCG                                                                                                                                         >  2:789517/1‑143
  gcgtagCCTGAATCTGAGGCAGCACCTGGCACGGCTGTGGCGGAAGTCGCTGTCGTGCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGC                                                                                                                                       <  2:556192/137‑1
  GCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGC                                                                                                                                       <  1:641181/143‑1
   CATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCA                                                                                                                                      <  1:647286/143‑1
    ATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATACGTTGGAGTCATTACCCAGCAC                                                                                                                                     >  2:622210/1‑143
       ACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAA                                                                                                                                  <  2:818888/143‑1
           GAATCTGGGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAA                                                                                                                              <  1:596785/143‑1
             gTCTGAGGTAGCACCTGGCGCGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAAGCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAG                                                                                                                            <  2:199387/142‑1
              TCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGA                                                                                                                           >  1:534223/1‑143
              TCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGA                                                                                                                           >  1:878229/1‑143
              TCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGGCGCTGTCGTTCTCCACATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGCCATTACCCGGCACACAATAAAGA                                                                                                                           >  1:374654/1‑143
               cgggGGCCGCACCTAGCACGGCTGGGACGGAAGTCGCTGTCGTGCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACAGAAAACAATATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAA                                                                                                                          <  2:849561/139‑1
               CTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAA                                                                                                                          <  1:719940/143‑1
               CTGAGGCAGCACCTCGCCCGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAA                                                                                                                          <  1:228162/143‑1
                  AGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTAATTACCCGGCACAAAATACAAAACAA                                                                                                                       >  2:698237/1‑143
                           CTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATT                                                                                                              >  1:181160/1‑143
                                ACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTA                                                                                                         >  2:619600/1‑143
                                        GACGGAAGTCGCTTTCGTTCTCAAAATCGGTAGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTG                                                                                                 <  2:189813/143‑1
                                         ACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGG                                                                                                >  2:631756/1‑143
                                             AAGACGCAGACGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTAT                                                                                            <  2:874832/143‑1
                                               GTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTG                                                                                          <  1:522780/143‑1
                                                TCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGC                                                                                         >  2:599335/1‑143
                                                  GCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCAC                                                                                       >  1:540741/1‑143
                                                         TTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGTACAACTAAA                                                                                >  2:524512/1‑143
                                                          TCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAAg                                                                               >  2:371122/1‑142
                                                                     GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACGGAATTGAAGGCTCTA                                                                    >  2:447152/1‑143
                                                                               ATGACAAAGTAATCGGGCATTATCTGAACATAAAACACTATCAACAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTCTGAATTCCTTACTTTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTC                                                          <  2:320585/143‑1
                                                                                 GACAAAGTCATCGTGCATTATCTGAACATAAAACACTATCAATAAGTGAGAGTCATTACCCAGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAA                                                        <  1:738645/143‑1
                                                                                    AAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTCCATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAA                                                     >  2:57023/1‑143
                                                                                       GTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAGGCACAAAATAAAGAACAATTTTGAATACATTACATACCTGGCTATTGCAAAACTCAATTTAAGGCTCTATTATTACCTAAACAgcac                                                  >  2:234204/1‑139
                                                                                         CATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGGACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCAC                                                >  2:453940/1‑143
                                                                                         CATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCAC                                                <  1:312764/143‑1
                                                                                                       TGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTACGGCTCTATTATTAACTCAACAAACCACCCCAATATAAGatc                                  >  2:487467/1‑140
                                                                                                        GAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATACGTTTG                                 >  2:853751/1‑143
                                                                                                         AACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGA                                <  2:194588/143‑1
                                                                                                          ACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAG                               <  2:820019/143‑1
                                                                                                              AAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTCTTACCTCAACAAACCACCCCAATATAAGTTTGAGATTA                           >  2:881530/1‑143
                                                                                                              AAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCCAATATTCCCTCAACAAACCACCCCAATATAAGTTTGAGATTA                           <  1:173104/143‑1
                                                                                                                AACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTCCATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATCACCGCAACAAACCACCCCAATATCAATTGGAGATgaat                         >  2:83847/1‑139
                                                                                                                        CAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAG                 <  2:503782/143‑1
                                                                                                                        CAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTCCACAACTGAATTTAAGTCTCTATTATTACCTCAACAAACAACCACAATATAAGTTTGAGATTACTACAATGAG                 >  1:40882/1‑143
                                                                                                                         AATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGCTTACTACAATGAGC                >  1:759693/1‑143
                                                                                                                           TAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTCCAATGAGCGA              >  1:794088/1‑143
                                                                                                                                       ATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAAT  >  1:32053/1‑143
                                                                                                                                                                                                                                                                                      
CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/258048‑257908
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAAT  <  NC_000913/1293039‑1292903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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