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
A6 F28 I1 R1 132 61.4 2079690 99.1% 2060972 139.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,293,009 G→A C109C (TGC→TGT)  rsmI ← 16S rRNA 2'‑O‑ribose C1402 methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,293,0090GA100.0% 199.3 / NA 58C109C (TGC→TGT) rsmI16S rRNA 2'‑O‑ribose C1402 methyltransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/31);  total (27/31)

ATCACGGCGGCCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGGCAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTTTGTTGTTCGTTATGGTCGTGCAGCG  >  NC_000913/3292874‑3293145
                                                                                                                                       |                                                                                                                                        
aTCACGGCGGCCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAgg                                                                                                                                      <  2:751244/140‑1 (MQ=255)
 tCACGGCGGCCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGt                                                                                                                                     <  2:676005/140‑1 (MQ=255)
   aCGGCGGCCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGTGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTAc                                                                                                                                   <  2:581516/140‑1 (MQ=255)
     ggcggcCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGc                                                                                                                                 >  2:210735/1‑140 (MQ=255)
      gcggcCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCa                                                                                                                                <  2:962056/140‑1 (MQ=255)
       cggcCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCAc                                                                                                                               >  1:752456/1‑140 (MQ=255)
        ggcCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCAcc                                                                                                                              <  1:815465/140‑1 (MQ=255)
        ggcCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCAcc                                                                                                                              <  1:855143/140‑1 (MQ=255)
            ttttGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGAt                                                                                                                          >  1:413636/1‑140 (MQ=255)
             tttGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATg                                                                                                                         <  2:686472/140‑1 (MQ=255)
             tttGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATg                                                                                                                         <  1:445142/140‑1 (MQ=255)
             tttGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATg                                                                                                                         <  1:863677/140‑1 (MQ=255)
             tttGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATg                                                                                                                         <  1:704441/140‑1 (MQ=255)
                      gCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAgg                                                                                                                <  2:709538/140‑1 (MQ=255)
                       cAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGa                                                                                                               <  2:370514/140‑1 (MQ=255)
                          gTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCg                                                                                                            <  1:175462/140‑1 (MQ=255)
                                    ttCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAgcg                                                                                                  >  1:93195/1‑140 (MQ=255)
                                    ttCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAgcg                                                                                                  >  2:18803/1‑140 (MQ=255)
                                    ttCGTAACAGAAACGGTCAGAGGGAAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAgcg                                                                                                  >  2:792574/1‑140 (MQ=255)
                                     tCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAgcgg                                                                                                 >  2:410105/1‑140 (MQ=255)
                                     tCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAgcgg                                                                                                 >  1:642506/1‑140 (MQ=255)
                                     tCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGGAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAgcgg                                                                                                 >  2:1019761/1‑140 (MQ=255)
                                          aCAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTc                                                                                            <  1:670886/140‑1 (MQ=255)
                                          aCAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTc                                                                                            >  1:50875/1‑140 (MQ=255)
                                                  ggTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTGCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCg                                                                                    <  2:413636/140‑1 (MQ=255)
                                                   gTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCgg                                                                                   >  1:113912/1‑140 (MQ=255)
                                                             aaaCCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAgcgc                                                                         <  2:752456/140‑1 (MQ=255)
                                                              aaCCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCa                                                                        <  2:602237/140‑1 (MQ=255)
                                                                cccGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAAt                                                                      >  1:216742/1‑140 (MQ=255)
                                                                     tGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGtttt                                                                 >  2:465622/1‑140 (MQ=255)
                                                                       cgcTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGc                                                               <  2:642506/140‑1 (MQ=255)
                                                                       cgcTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGc                                                               <  1:188652/140‑1 (MQ=255)
                                                                         cTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGccc                                                             >  2:4898/1‑140 (MQ=255)
                                                                              cGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCtt                                                        >  1:580590/1‑140 (MQ=255)
                                                                               gCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTg                                                       <  2:564995/140‑1 (MQ=255)
                                                                                      tAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTc                                                >  1:785359/1‑140 (MQ=255)
                                                                                        gcagcaCACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGc                                              >  2:795182/1‑140 (MQ=255)
                                                                                            cacaCGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCcagc                                          <  2:235067/140‑1 (MQ=255)
                                                                                             acacGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCcagca                                         <  1:930572/140‑1 (MQ=255)
                                                                                             acacGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCcagca                                         >  1:230439/1‑140 (MQ=255)
                                                                                               acGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCagcagc                                       >  1:253729/1‑140 (MQ=255)
                                                                                               acGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCagcagc                                       >  2:720323/1‑140 (MQ=255)
                                                                                                  gCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGtt                                    >  1:228103/1‑140 (MQ=255)
                                                                                                  gCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGtt                                    >  1:540868/1‑140 (MQ=255)
                                                                                                   cccGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGttt                                   >  2:1014928/1‑140 (MQ=255)
                                                                                                   cccGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGttt                                   >  2:978909/1‑140 (MQ=255)
                                                                                                     cGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCa                                 <  1:792574/140‑1 (MQ=255)
                                                                                                     cGGGTAGCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCa                                 <  1:410105/140‑1 (MQ=255)
                                                                                                           gCGGCACCACGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCtttt                           >  1:684684/1‑140 (MQ=255)
                                                                                                               caccacGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTttgtt                       <  1:1019761/140‑1 (MQ=255)
                                                                                                                accacGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTttgttg                      <  1:423283/140‑1 (MQ=255)
                                                                                                                accacGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTttgttg                      <  1:969654/140‑1 (MQ=255)
                                                                                                                accacGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTttgttg                      <  1:18803/140‑1 (MQ=255)
                                                                                                                accacGCGGATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTttgttg                      <  2:113912/140‑1 (MQ=255)
                                                                                                                       ggATCCCCGCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTTTGTTGTTCGTTa               <  1:4898/140‑1 (MQ=255)
                                                                                                                          tCCCCGCTTCACGACAGGTACGCGCCAGATGGTGGCCAGGATCGTTAATTAACGGCGGTCCGGCGTCGGAAACCATAGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTTAGCTTTTTGTTTTTCGTTAtag            <  2:952599/140‑3 (MQ=255)
                                                                                                                               gCTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTTTGTTGTTCGTTATGGTCGTg       >  1:818706/1‑140 (MQ=255)
                                                                                                                                cTTCACGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTTTGTTGTTCGTTATGGTCGTGc      >  2:442610/1‑140 (MQ=255)
                                                                                                                                    aCGACAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTTTGTTGTTCGTTATGGTCGTGCAgcg  <  1:268710/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                        
ATCACGGCGGCCTTTTGATTTGGCAGGTAAAAAGCCTTCGTAACAGAAACGGTCAGAGGGTAAACCCGCTGCGCTTAACGCAGTGATAGCAGCACACGGCCCGGGTAGCGGCACCACGCGGATCCCCGCTTCACGGCAGGTACGCACCAGATGGTAGCCAGGATCGTTAATTAGCGGCGTTCCGGCATCGGAAACCAGCGCAATGTTTTGCCCCTCTTGCAGCTTCGCCAGCAGCGTTTCAGCTTTTTGTTGTTCGTTATGGTCGTGCAGCG  >  NC_000913/3292874‑3293145

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A