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 F50 I2 R1 193 39.9 1341687 91.8% 1231668 149.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 576,168 T→C pseudogene (658/1040 nt) nmpC ← DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913576,1680TC100.0% 151.0 / NA 42pseudogene (658/1040 nt)nmpCDLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/22);  total (20/22)

TCAGCAAATACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGTGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGTACTGAGCAGC  >  NC_000913/576020‑576312
                                                                                                                                                    |                                                                                                                                                
tCAGCAAATACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAgcgt                                                                                                                                                >  2:77781/1‑151 (MQ=255)
  aGCAAATACAGTCATATGCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCGTATTTCAGACCTGCAGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCg                                                                                                                                              >  1:516905/1‑151 (MQ=255)
   gCAAATACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCgg                                                                                                                                             >  1:86307/1‑151 (MQ=255)
     aaaTACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGt                                                                                                                                            >  2:566678/1‑150 (MQ=255)
      aaTACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTAc                                                                                                                                          >  2:507147/1‑151 (MQ=255)
         aCAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGa                                                                                                                                        <  1:343985/150‑1 (MQ=255)
          cAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATc                                                                                                                                      <  2:122964/151‑1 (MQ=255)
            gTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAg                                                                                                                                    <  2:537294/151‑1 (MQ=255)
                tatTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGAttt                                                                                                                                >  2:229094/1‑151 (MQ=255)
                      gggTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGc                                                                                                                             <  2:381777/148‑1 (MQ=255)
                            cAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATa                                                                                                                          <  2:54085/145‑1 (MQ=255)
                            cAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATa                                                                                                                          >  1:54086/1‑145 (MQ=255)
                                aTAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCg                                                                                                                <  2:126720/151‑1 (MQ=255)
                                aTAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCg                                                                                                                <  2:505851/151‑1 (MQ=255)
                                         ggCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAAt                                                                                                       >  2:250304/1‑151 (MQ=255)
                                           ccAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATcc                                                                                                     <  2:343412/151‑1 (MQ=255)
                                             aGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGTATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACGTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCtt                                                                                                   <  2:355878/151‑1 (MQ=255)
                                             aGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCtt                                                                                                   <  1:491534/151‑1 (MQ=255)
                                              ggTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTc                                                                                                  <  2:308462/151‑1 (MQ=255)
                                                   aTGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTAtt                                                                                             >  1:296145/1‑151 (MQ=255)
                                                       tgttAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCTTTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTTCACCGATACCGAATCCTTCGTATTCAt                                                                                          <  2:37705/150‑1 (MQ=255)
                                                            gCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGt                                                                                      >  2:125350/1‑149 (MQ=255)
                                                                cATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGc                                                                                   >  1:168468/1‑148 (MQ=255)
                                                                 atatTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCag                                                                                 >  2:327862/1‑149 (MQ=255)
                                                                 atatTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCag                                                                                 >  2:600941/1‑149 (MQ=255)
                                                                     ttCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAAc                                                                           >  2:567671/1‑151 (MQ=255)
                                                                      tCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAAc                                                                           <  1:61791/150‑1 (MQ=255)
                                                                       cAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAAcc                                                                          <  2:508465/150‑1 (MQ=255)
                                                                        aGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCg                                                                         >  2:302805/1‑150 (MQ=255)
                                                                                  cccAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCAcc                                                              <  2:36853/151‑1 (MQ=255)
                                                                                         ttCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCt                                                       >  1:401373/1‑151 (MQ=255)
                                                                                          tCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCt                                                       <  2:618234/150‑1 (MQ=255)
                                                                                                 ttttACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAgtgt                                                <  2:81937/150‑1 (MQ=255)
                                                                                                  tttACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTa                                               <  1:17463/150‑1 (MQ=255)
                                                                                                  tttACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTa                                               <  2:232393/150‑1 (MQ=255)
                                                                                                           aGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGaa                                      >  2:39683/1‑150 (MQ=255)
                                                                                                              aaaTACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCg                                  >  2:253065/1‑151 (MQ=255)
                                                                                                                     tCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGAATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACg                             <  1:139719/149‑1 (MQ=255)
                                                                                                                         gaagaaCTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGtt                       <  2:225680/151‑1 (MQ=255)
                                                                                                                         gaagaaCTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGtt                       <  2:401377/151‑1 (MQ=255)
                                                                                                                                     cTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGt            >  2:501380/1‑150 (MQ=255)
                                                                                                                                     cTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGt            >  1:177915/1‑150 (MQ=255)
                                                                                                                                              cTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGTACTGagcagc  >  2:3103/1‑151 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
TCAGCAAATACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGTGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGTACTGAGCAGC  >  NC_000913/576020‑576312

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A