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
A7 F1 I2 R1 94 59.5 3027142 91.9% 2781943 108.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,440,113 A→G V306A (GTG→GCG)  rpoA ← RNA polymerase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,440,1130AG100.0% 213.6 / NA 57V306A (GTG→GCG) rpoARNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/30);  total (27/30)

GCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAG  >  NC_000913/3439994‑3440235
                                                                                                                       |                                                                                                                          
gcgcATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAag                                                                                                         >  1:741728/1‑139 (MQ=255)
gcgcATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAag                                                                                                         >  1:72182/1‑139 (MQ=255)
gcgcATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAag                                                                                                         >  1:395888/1‑139 (MQ=255)
gcgcATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAag                                                                                                         >  1:36096/1‑139 (MQ=255)
            aTCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTAcc                                                                                             <  2:1167298/139‑1 (MQ=255)
                  ctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCTAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGtt                                                                                       >  1:1165163/1‑139 (MQ=255)
                  ctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGtt                                                                                       >  2:1102181/1‑139 (MQ=255)
                  ctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGtt                                                                                       >  1:379548/1‑139 (MQ=255)
                  ctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTAACAAGGtt                                                                                       >  1:1353100/1‑139 (MQ=255)
                       tAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCg                                                                                  >  1:312145/1‑139 (MQ=255)
                                 aCCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg                                                                                     <  2:1188056/126‑1 (MQ=255)
                                 aCCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg                                                                                     >  1:1188056/1‑126 (MQ=255)
                                      tgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg                                                                                     <  2:99009/121‑1 (MQ=255)
                                      tgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg                                                                                     >  1:99009/1‑121 (MQ=255)
                                      tgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTa                                                                             >  2:1355672/1‑129 (MQ=255)
                                      tgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTa                                                                             <  1:1355672/129‑1 (MQ=255)
                                           cGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCaa                                                                   >  2:751341/1‑134 (MQ=255)
                                           cGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCaa                                                                   <  1:751341/134‑1 (MQ=255)
                                           cGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCg                                                              <  1:1102181/139‑1 (MQ=255)
                                           cGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCg                                                              <  1:791669/139‑1 (MQ=255)
                                             gTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAAtct                                                                                                                >  1:228062/1‑87 (MQ=255)
                                             gTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAAtct                                                                                                                <  2:228062/87‑1 (MQ=255)
                                              ttACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTa                                                           <  2:741728/139‑1 (MQ=255)
                                              ttACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTa                                                           <  2:526972/139‑1 (MQ=255)
                                                aCTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAAt                                                                                                                  <  1:1489771/82‑1 (MQ=255)
                                                aCTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAAt                                                                                                                  >  2:1489771/1‑82 (MQ=255)
                                                aCTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACg                                                         <  2:395888/139‑1 (MQ=255)
                                                aCTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACg                                                         <  2:312145/139‑1 (MQ=255)
                                                 cTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGATAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGc                                                        <  2:1430689/139‑1 (MQ=255)
                                                 cTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGc                                                        <  2:147999/139‑1 (MQ=255)
                                                      cAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTAc                                                   <  2:72182/139‑1 (MQ=255)
                                                           aTGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGAt                                              <  2:408684/139‑1 (MQ=255)
                                                            tGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATc                                             >  2:427270/1‑139 (MQ=255)
                                                              cTTGCCGGTGGCTAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAc                                           <  2:1165163/139‑1 (MQ=255)
                                                              cTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAc                                           <  2:1353100/139‑1 (MQ=255)
                                                              cTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAc                                           >  1:539945/1‑139 (MQ=255)
                                                                   cGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGata                                      <  2:379548/139‑1 (MQ=255)
                                                                      tGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCg                                                              >  1:864232/1‑112 (MQ=255)
                                                                      tGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTCTAAGGAGCTCAACCTCg                                                              <  2:864232/112‑1 (MQ=255)
                                                                         ccAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTgg                                <  2:747929/139‑1 (MQ=255)
                                                                                 ccAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTc                        <  1:427270/139‑1 (MQ=255)
                                                                                 ccAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTc                        <  2:36096/139‑1 (MQ=255)
                                                                                  cAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCt                       >  1:1129022/1‑139 (MQ=255)
                                                                                       gcATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg                                                                                     <  1:1322840/72‑1 (MQ=255)
                                                                                       gcATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAg                                                                                     >  2:1322840/1‑72 (MQ=255)
                                                                                       gcATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTc                                                                     <  1:583802/88‑1 (MQ=255)
                                                                                       gcATGCCCAGAGACAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCACTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTc                                                                     >  2:583802/1‑88 (MQ=255)
                                                                                                  gaCAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCtt                         >  2:761388/1‑121 (MQ=255)
                                                                                                  gaCAGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCtt                         <  1:761388/121‑1 (MQ=255)
                                                                                                     aGTCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCag    >  1:285172/1‑139 (MQ=255)
                                                                                                       tCCACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCagag  >  2:1072973/1‑139 (MQ=255)
                                                                                                        ccACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAg               >  1:807432/1‑125 (MQ=255)
                                                                                                        ccACGGGAAGCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAg               <  2:807432/125‑1 (MQ=255)
                                                                                                                 gCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACg                                                         <  1:1382219/74‑1 (MQ=255)
                                                                                                                 gCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACg                                                         >  2:113879/1‑74 (MQ=255)
                                                                                                                 gCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACg                                                         >  2:1382219/1‑74 (MQ=255)
                                                                                                                 gCCAGCGCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACg                                                         <  1:113879/74‑1 (MQ=255)
                                                                                                                       |                                                                                                                          
GCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAG  >  NC_000913/3439994‑3440235

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A