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 F1 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,623,101 C→T *339* (TAG→TAA)  lplA ← lipoate‑protein ligase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,623,1010CT100.0% 176.1 / NA 55*339* (TAG→TAA) lplAlipoate‑protein ligase A
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (23/32);  total (23/32)

ATCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAACTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGTTGCAGCATATCTGCGCGGTACAGG  >  NC_000913/4622966‑4623215
                                                                                                                                       |                                                                                                                  
aTCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTAc                                                                                                                 >  2:1629847/1‑139 (MQ=255)
 tCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCTGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTAcc                                                                                                                >  2:1393141/1‑139 (MQ=255)
 tCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTAcc                                                                                                                >  2:162237/1‑139 (MQ=255)
 tCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTAcc                                                                                                                >  2:1120140/1‑139 (MQ=255)
      cTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACa                                                                                                           >  1:1168182/1‑139 (MQ=255)
       tGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAg                                                                                                          <  1:1188756/139‑1 (MQ=255)
        ggCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGc                                                                                                         <  1:1120140/139‑1 (MQ=255)
        ggCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGc                                                                                                         <  1:881890/139‑1 (MQ=255)
        ggCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGc                                                                                                         <  1:162237/139‑1 (MQ=255)
                agTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGcca                                                                                                 <  1:131646/139‑1 (MQ=255)
                      ggCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATg                                                                                           <  2:1168182/139‑1 (MQ=255)
                      ggCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATg                                                                                           <  1:58556/139‑1 (MQ=255)
                         aaaCGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGATATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCg                                                                                        <  2:976609/139‑1 (MQ=255)
                          aaCGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGTGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGccccc                                                                                                     >  1:1383117/1‑125 (MQ=255)
                          aaCGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGTGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGccccc                                                                                                     <  2:1383117/125‑1 (MQ=255)
                            cGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATg                                                                                           <  2:1812740/133‑1 (MQ=255)
                            cGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATg                                                                                           >  1:1812740/1‑133 (MQ=255)
                              gTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAAc                                                                                   >  1:152720/1‑139 (MQ=255)
                               tCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACt                                                                                  >  2:329676/1‑139 (MQ=255)
                                    agagATCCGCGTATCAGCGAGGCGTTCCGCCACATCGCCCACGAAATTGCGGAAAAAACCCGGCAAATCGAAGAGAAAGTTGCCCGCATTGGCGGGTAATTCCCTTAGAGTCCCCGCAACCCATGCCGATAACTCCCGt                                                                             <  1:47551/139‑1 (MQ=255)
                                     gagaTCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCTGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTa                                                                            <  1:1393141/139‑1 (MQ=255)
                                             cgTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCtttt                                                                    >  2:1012107/1‑139 (MQ=255)
                                                       aGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCg                                                          <  1:329676/139‑1 (MQ=255)
                                                        ggCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCgg                                                         >  1:1007129/1‑139 (MQ=255)
                                                          cGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGa                                                       <  2:770678/139‑1 (MQ=255)
                                                          cGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGa                                                       <  1:1545657/139‑1 (MQ=255)
                                                            tttCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAg                                                     <  1:1629847/139‑1 (MQ=255)
                                                             ttCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGc                                                                                                         >  2:899303/1‑86 (MQ=255)
                                                             ttCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGc                                                                                                         <  1:899303/86‑1 (MQ=255)
                                                                       tGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAg                                          <  2:864860/139‑1 (MQ=255)
                                                                         cgcAAGAAATGCCGGAAAGAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAAc                                                                                   >  2:1207232/1‑96 (MQ=255)
                                                                         cgcAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGa                                                       <  2:942677/124‑1 (MQ=255)
                                                                         cgcAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGa                                                       >  1:942677/1‑124 (MQ=255)
                                                                         cgcAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAACTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAAc                                                                                   <  1:1207232/96‑1 (MQ=255)
                                                                           cAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCt                                      <  2:1007129/139‑1 (MQ=255)
                                                                               aaaTGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGc                                  <  2:152720/139‑1 (MQ=255)
                                                                                 aTGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCg                                   <  2:1279091/136‑1 (MQ=255)
                                                                                 aTGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCg                                   >  1:1279091/1‑136 (MQ=255)
                                                                                       gAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGt                          <  1:1361388/139‑1 (MQ=255)
                                                                                                  gCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTa                                                                                                             <  1:1652159/45‑1 (MQ=255)
                                                                                                  gCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAATTACCTTa                                                                                                             >  2:1652159/1‑45 (MQ=255)
                                                                                                              gaAAGTTGCCCGCATGGGGGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTc                                                                  >  1:1019488/1‑76 (MQ=255)
                                                                                                              gaAAGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTc                                                                  <  2:1019488/76‑1 (MQ=255)
                                                                                                               aaaGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGTTGCAGCATATCTGCGCGGTACAgg  <  2:1549570/139‑1 (MQ=255)
                                                                                                               aaaGTTGCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCCGTTGCAGCATATCTGCGCGGTACAgg  >  1:1549570/1‑139 (MQ=255)
                                                                                                                     gCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTc                                                                  <  1:927430/69‑1 (MQ=255)
                                                                                                                     gCCCGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTc                                                                  >  2:927430/1‑69 (MQ=255)
                                                                                                                      cccGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCCTTTTCCTGTTCCg                                                          <  2:1557938/76‑1 (MQ=255)
                                                                                                                      cccGCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCCTTTTCCTGTTCCg                                                          >  1:1557938/1‑76 (MQ=255)
                                                                                                                         gCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGa                                                       >  2:180340/1‑76 (MQ=255)
                                                                                                                         gCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGa                                                       >  1:977086/1‑76 (MQ=255)
                                                                                                                         gCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGa                                                       <  1:180340/76‑1 (MQ=255)
                                                                                                                         gCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGa                                                       <  2:977086/76‑1 (MQ=255)
                                                                                                                         gCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGt                          >  1:869273/1‑105 (MQ=255)
                                                                                                                         gCATGGGCGGGTAATTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGt                          <  2:869273/105‑1 (MQ=255)
                                                                                                                                       |                                                                                                                  
ATCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAACTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGTTGCAGCATATCTGCGCGGTACAGG  >  NC_000913/4622966‑4623215

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A