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 I1 R1 83 73.5 3575638 92.3% 3300313 107.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,426,492 A→G R99R (CGT→CGC)  hisJ ← histidine ABC transporter periplasmic binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,426,4920AG100.0% 236.3 / NA 63R99R (CGT→CGC) hisJhistidine ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/35);  total (28/35)

GGGTGGTGCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGACGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATA  >  NC_000913/2426359‑2426613
                                                                                                                                     |                                                                                                                         
gggTGGTGCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGttt                                                                                                                      <  2:1610737/139‑1 (MQ=255)
  gtggtgCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGttttt                                                                                                                    <  2:1777413/139‑1 (MQ=255)
   tggtgCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTc                                                                                                                   >  2:459187/1‑139 (MQ=255)
     gtgCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTcc                                                                                                                  >  1:378184/1‑138 (MQ=255)
     gtgCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTcc                                                                                                                  <  2:378184/138‑1 (MQ=255)
      tgCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGt                                                                                                                >  2:1392134/1‑139 (MQ=255)
      tgCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGt                                                                                                                >  2:936976/1‑139 (MQ=255)
      tgCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGt                                                                                                                >  1:1295993/1‑139 (MQ=255)
       gCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTa                                                                                                               <  1:82202/139‑1 (MQ=255)
           tGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATgg                                                                                                           >  2:1278312/1‑139 (MQ=255)
            gCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                          <  1:219678/139‑1 (MQ=255)
                       aCCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACa                                                                                               >  1:1272935/1‑139 (MQ=255)
                             ttGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATgg                                                                                         <  1:636506/139‑1 (MQ=255)
                                   ttCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGa                                                                                                    <  2:609531/122‑1 (MQ=255)
                                   ttCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGa                                                                                                    >  1:609531/1‑122 (MQ=255)
                                          actcgactGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATcttctt                                                                            >  2:972976/1‑139 (MQ=255)
                                                     ggCTGAATGTCAGAATTTTTCGCCACCCCCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAgg                                                                 <  1:459187/139‑1 (MQ=255)
                                                     ggCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                          <  1:1380623/98‑1 (MQ=255)
                                                     ggCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                          >  2:1380623/1‑98 (MQ=255)
                                                      gCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGa                                                                <  1:877632/139‑1 (MQ=255)
                                                                    tttttCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                          >  2:614701/1‑83 (MQ=255)
                                                                    tttttCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                          <  1:614701/83‑1 (MQ=255)
                                                                         cGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGc                                             <  1:178232/139‑1 (MQ=255)
                                                                         cGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGc                                             <  2:184502/139‑1 (MQ=255)
                                                                            caccaccaAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTa                                                                                                               >  2:858/1‑70 (MQ=255)
                                                                            caccaccaAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTa                                                                                                               <  1:858/70‑1 (MQ=255)
                                                                            caccaccaAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGa                                          >  1:199944/1‑139 (MQ=255)
                                                                                 ccaAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACatgat                                                                                           >  2:1066896/1‑85 (MQ=255)
                                                                                 ccaAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTc                                     <  2:1295993/139‑1 (MQ=255)
                                                                                 ccaAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTCTTCCGTAATGGAAAGCGATGACatgat                                                                                           <  1:1066896/85‑1 (MQ=255)
                                                                                 ccaAACGAGAATCGACAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTc                                     <  2:496561/139‑1 (MQ=255)
                                                                                   aaaCGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGATGGGATTAACGCATCCAGCGGATTTTCGa                                   <  2:1106808/139‑1 (MQ=255)
                                                                                   aaaCGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGa                                   <  1:972976/139‑1 (MQ=255)
                                                                                     aCGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACa                                 <  1:902044/139‑1 (MQ=255)
                                                                                     aCGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACa                                 <  1:1413204/139‑1 (MQ=255)
                                                                                          aaTCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGt                            >  1:1243782/1‑139 (MQ=255)
                                                                                           aTCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTa                           <  1:936976/139‑1 (MQ=255)
                                                                                                   cGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGttt                                                                                                                      <  2:33363/40‑1 (MQ=255)
                                                                                                   cGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGttt                                                                                                                      >  1:33363/1‑40 (MQ=255)
                                                                                                     tACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTAt                 >  2:1592454/1‑139 (MQ=255)
                                                                                                        aGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGa              <  2:1243782/139‑1 (MQ=255)
                                                                                                        aGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGa              <  1:1392134/139‑1 (MQ=255)
                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGc                                                                                                      <  2:403069/46‑1 (MQ=255)
                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGc                                                                                                      >  1:403069/1‑46 (MQ=255)
                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGAc                                                                                                <  1:1615209/52‑1 (MQ=255)
                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGAc                                                                                                >  2:1615209/1‑52 (MQ=255)
                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGt         >  2:1201415/1‑139 (MQ=255)
                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTGCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGt         <  1:1278312/139‑1 (MQ=255)
                                                                                                              tCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGtt        >  1:1672523/1‑139 (MQ=255)
                                                                                                               cGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGttt       <  2:49886/139‑1 (MQ=255)
                                                                                                               cGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGttt       >  2:253396/1‑139 (MQ=255)
                                                                                                                  tGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCa    >  1:685572/1‑139 (MQ=255)
                                                                                                                    aaGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCtttt                                                                     >  2:162580/1‑72 (MQ=255)
                                                                                                                    aaGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCtttt                                                                     <  1:162580/72‑1 (MQ=255)
                                                                                                                    aaGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGc                                             <  1:1105585/96‑1 (MQ=255)
                                                                                                                    aaGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATa  <  2:199944/139‑1 (MQ=255)
                                                                                                                    aaGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATa  <  1:1604591/139‑1 (MQ=255)
                                                                                                                    aaGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATa  >  1:1346057/1‑139 (MQ=255)
                                                                                                                    aaGGCTATTTCTTGCTGGCGTTTTTCCGCAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGc                                             >  2:1105585/1‑96 (MQ=255)
                                                                                                                                 gCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACAtt                       >  2:774331/1‑105 (MQ=255)
                                                                                                                                 gCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACAtt                       <  1:774331/105‑1 (MQ=255)
                                                                                                                                  cTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCtttt                                                                     >  2:303575/1‑58 (MQ=255)
                                                                                                                                  cTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCtttt                                                                     <  1:303575/58‑1 (MQ=255)
                                                                                                                                     |                                                                                                                         
GGGTGGTGCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGACGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATA  >  NC_000913/2426359‑2426613

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