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 F28 I1 R1 183 98.6 3427438 96.9% 3321187 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,060,280 (T)9→8 intergenic (+50/‑167) bipA → / → yihL ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,060,2720T.96.4% 213.8 / 2.7 55intergenic (+42/‑175)bipA/yihLribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base . (22/31);  total (23/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

ACTGGTAGAAGTGACTCCGACCTCTATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTGCAAAGTCATACGCCGTTAATTGCTTTCTTTTTTGGCGTAAGC  >  NC_000913/4060134‑4060406
                                                                                                                                          |                                                                                                                                      
aCTGGTAGAAGTGACTCCGACCTCTATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGtt                                                                                                                                       >  2:1711434/1‑140 (MQ=255)
   ggTAGAAGTGACTCCGACCTCTATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGttttt                                                                                                                                    <  1:1711434/140‑1 (MQ=255)
              cTCCGACCTCTATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCg                                                                                                                        >  1:1203283/1‑140 (MQ=255)
              cTCCGACCTCTATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCg                                                                                                                        >  1:12996/1‑140 (MQ=255)
               tCCGACCTCTATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGt                                                                                                                       >  2:838084/1‑140 (MQ=255)
                        tATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTTGCCTGTCGTGAGCGcac                                                                                                               <  1:1076351/140‑1 (MQ=255)
                        tATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTTGCCTGTCGTGAGCGcac                                                                                                               >  2:1076351/1‑140 (MQ=255)
                         aTCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCacac                                                                                                             <  1:248075/140‑1 (MQ=255)
                         aTCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCacac                                                                                                             <  2:12996/140‑1 (MQ=255)
                          tCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCGCCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACAcc                                                                                                            <  1:779395/140‑1 (MQ=255)
                                ttCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGt                                                                                                                       <  1:1481992/123‑1 (MQ=255)
                                ttCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGt                                                                                                                       >  2:1481992/1‑123 (MQ=255)
                                ttCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCg                                                                                                      >  1:980842/1‑140 (MQ=255)
                                  cGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAg                                                                                                    >  2:357647/1‑140 (MQ=255)
                                  cGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAg                                                                                                    >  2:711469/1‑140 (MQ=255)
                                  cGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAg                                                                                                    <  2:930548/140‑1 (MQ=255)
                                  cGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAg                                                                                                    >  1:363921/1‑140 (MQ=255)
                                  cGTAAACGTCACCTGACGGAAAACGATCGGCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAAGGCGAg                                                                                                    >  2:245740/1‑140 (MQ=255)
                                    tAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTa                                                                                                  >  1:930371/1‑140 (MQ=255)
                                    tAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTa                                                                                                  >  2:1395709/1‑140 (MQ=255)
                                    tAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTa                                                                                                  >  2:219669/1‑140 (MQ=255)
                                      aaacgccccTGAAGGAAAACGATCCTCGCCGGGGCAACCGCGCACCGAAAAACCATTAATTTCGTTTTTTAGTCAAAAAAAACCTGGCAGGGATTGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtc                                                                                                <  2:1485536/133‑1 (MQ=255)
                                      aaCGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtc                                                                                                <  2:1638343/140‑1 (MQ=255)
                                      aaCGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtc                                                                                                <  2:1074826/140‑1 (MQ=255)
                                      aaCGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtc                                                                                                <  1:1208042/140‑1 (MQ=255)
                                        cGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtctc                                                                                              >  2:958739/1‑140 (MQ=255)
                                        cGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtctc                                                                                              <  1:461996/140‑1 (MQ=255)
                                        cGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtctc                                                                                              <  1:1395709/140‑1 (MQ=255)
                                           cACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtc                                                                                                >  2:1593036/1‑135 (MQ=255)
                                           cACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTAtc                                                                                                <  1:1593036/135‑1 (MQ=255)
                                           cACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCt                                                                                           >  1:180955/1‑140 (MQ=255)
                                           cACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCt                                                                                           >  2:436995/1‑140 (MQ=255)
                                            aCCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCtt                                                                                          >  1:1334481/1‑140 (MQ=255)
                                                gACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATaa                                                                                      <  2:180955/140‑1 (MQ=255)
                                                 aCGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAg                                                                                     >  1:382479/1‑140 (MQ=255)
                                                 aCGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAg                                                                                     >  1:159660/1‑140 (MQ=255)
                                                  cGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGt                                                                                    >  2:600690/1‑140 (MQ=255)
                                                  cGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCAAACCAATGCGAGTATCTCCCTTATAAGt                                                                                    <  1:1623152/140‑1 (MQ=255)
                                                    gAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCt                                                                                  <  1:436995/140‑1 (MQ=255)
                                                    gAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCt                                                                                  <  2:288491/140‑1 (MQ=255)
                                                       aaCGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCtgtg                                                                               <  2:1203283/140‑1 (MQ=255)
                                                         cGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGt                                                                             <  2:363921/140‑1 (MQ=255)
                                                         cGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGt                                                                             <  2:193848/140‑1 (MQ=255)
                                                         cGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGt                                                                             <  2:1334481/140‑1 (MQ=255)
                                                           aTCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTa                                                                           <  1:1380187/140‑1 (MQ=255)
                                                                   cgcgCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATa                                                                   >  2:504577/1‑140 (MQ=255)
                                                                         aaCCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGc                                                             <  1:357647/140‑1 (MQ=255)
                                                                             gcgcACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTg                                                         <  1:600690/140‑1 (MQ=255)
                                                                                  ccGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTcaca                                                    <  1:838084/140‑1 (MQ=255)
                                                                                   cGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACaa                                                   >  2:401867/1‑140 (MQ=255)
                                                                                          cGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTg                                            <  2:382479/140‑1 (MQ=255)
                                                                                          cGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTg                                            <  2:1532400/140‑1 (MQ=255)
                                                                                                              tCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTGCAAAGTCATACGCCGTTAAt                        <  1:401867/140‑1 (MQ=255)
                                                                                                                 tAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTGCAAAGTCATACGCCGTTAATTGc                     >  2:189330/1‑140 (MQ=255)
                                                                                                                          tGCCAGCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTGCAAAGTCATACGCCGTTAATTGCTTTCttttt            <  1:189330/140‑1 (MQ=255)
                                                                                                                               gCGATGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTGCAAAGTCATACGCCGTTAATTGCTTTCTTTTTTGgcg       <  2:1638792/140‑1 (MQ=255)
                                                                                                                                   tGGCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTGCAAAGTCATACGCCGTTAATTGCTTTCTTTTTTGgcgtaag   <  2:930371/140‑1 (MQ=255)
                                                                                                                                    ggCAGGTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTGCAAAGTCATACGCCGTTAATTGCTTTCTTTTTTGgcgtaagc  <  1:399562/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                      
ACTGGTAGAAGTGACTCCGACCTCTATCCGTATTCGTAAACGTCACCTGACGGAAAACGATCGTCGCCGCGCCAACCGCGCACCGAAAGACGATTAATTTCGTTTTTTAGTCATAAAAAACCTGCCAGCGATGGCAGGTTTTTTTTTGCCTGTCGTGAGCGCACACCAATGCGAGTATCTCCCTTATAAGTCTGTGGTTACGTCAATAGAGAGCTTTGTCACAATTATCTGCAAAGTCATACGCCGTTAATTGCTTTCTTTTTTGGCGTAAGC  >  NC_000913/4060134‑4060406

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: 

GATK/CNVnator alignment

N/A