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
A4 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,913,699 C→T *434* (TAG→TAA)  rlmD ← 23S rRNA m(5)U1939 methyltransferase, SAM‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,913,6990CT100.0% 223.1 / NA 69*434* (TAG→TAA) rlmD23S rRNA m(5)U1939 methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/37);  total (32/37)

TCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGTCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAACTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCTGCTTTTAATAACGCTTCGCTATCCCGAGCCAGCGTTGCAG  >  NC_000913/2913564‑2913829
                                                                                                                                       |                                                                                                                                  
tCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTAt                                                                                                                                 >  2:960662/1‑139 (MQ=255)
    gctggTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTaa                                                                                                                             >  1:784534/1‑139 (MQ=255)
         tAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAAcgcgc                                                                                                                        <  2:660004/139‑1 (MQ=255)
             aCCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCgaga                                                                                                                    <  1:554857/139‑1 (MQ=255)
                  gACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAAcgcg                                                                                                                         >  2:514789/1‑129 (MQ=255)
                  gACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAAcgcg                                                                                                                         <  1:514789/129‑1 (MQ=255)
                       gCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCAt                                                                                                          >  1:1657045/1‑139 (MQ=255)
                        cGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATc                                                                                                         <  2:224098/139‑1 (MQ=255)
                             cATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCgag                                                                                                                     >  1:1105795/1‑122 (MQ=255)
                             cATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCgag                                                                                                                     <  2:1105795/122‑1 (MQ=255)
                                ttttCCGAATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAg                                                                                                 <  2:866369/139‑1 (MQ=255)
                                 tttCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGa                                                                                                <  2:1657045/139‑1 (MQ=255)
                                     cGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTc                                                                                            >  1:635961/1‑139 (MQ=255)
                                          cAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCgtg                                                                                       <  2:1066437/139‑1 (MQ=255)
                                                          aTTGATATGTGCACTTCTTACCGCGACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCa                                                                       >  1:1132038/1‑139 (MQ=255)
                                                                atGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCg                                                                                         >  2:836447/1‑115 (MQ=255)
                                                                atGTGCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCg                                                                                         <  1:836447/115‑1 (MQ=255)
                                                                 tgtgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGc                                                                <  2:635961/139‑1 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCAt                                                                                                          <  2:728307/95‑1 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCAt                                                                                                          >  1:728307/1‑95 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCAt                                                                                                          >  2:1569859/1‑95 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCAt                                                                                                          <  1:1569859/95‑1 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTc                                                                                            <  1:1589916/109‑1 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTc                                                                                            >  2:1589916/1‑109 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGtgtgtg                                                                                   <  2:62702/118‑1 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGtgtgtg                                                                                   >  1:62702/1‑118 (MQ=255)
                                                                   tgCACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGAGTGGGAACATATCCAGCATCGCCa                                                              >  1:1507979/1‑139 (MQ=255)
                                                                     cACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTAcc                                                                                                            <  1:1404338/91‑1 (MQ=255)
                                                                     cACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTAcc                                                                                                            >  2:1404338/1‑91 (MQ=255)
                                                                     cACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCa                                                                                                  <  1:902541/101‑1 (MQ=255)
                                                                     cACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCa                                                                                                  >  2:902541/1‑101 (MQ=255)
                                                                     cACTTCTTACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGt                                                            >  2:518911/1‑139 (MQ=255)
                                                                          cttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTc                                                                                            >  2:1620947/1‑102 (MQ=255)
                                                                          cttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTc                                                                                            <  1:1620947/102‑1 (MQ=255)
                                                                           ttACCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      <  1:118103/139‑1 (MQ=255)
                                                                             aCCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTcgcg                                                        <  2:917834/135‑1 (MQ=255)
                                                                             aCCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTcgcg                                                        >  1:917834/1‑135 (MQ=255)
                                                                             aCCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      >  1:452021/1‑137 (MQ=255)
                                                                             aCCGCAACCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      <  2:452021/137‑1 (MQ=255)
                                                                                  aaCCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      <  2:1423082/132‑1 (MQ=255)
                                                                                  aaCCATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      >  1:1423082/1‑132 (MQ=255)
                                                                                    ccATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACatat                                                                          >  2:1309023/1‑110 (MQ=255)
                                                                                    ccATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACatat                                                                          <  1:1309023/110‑1 (MQ=255)
                                                                                    ccATCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTatat                                             >  1:162408/1‑139 (MQ=255)
                                                                                       tCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCg                                                                                         >  1:1631940/1‑92 (MQ=255)
                                                                                       tCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCg                                                                                         <  2:1631940/92‑1 (MQ=255)
                                                                                       tCGCCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCt                                          <  1:1604753/139‑1 (MQ=255)
                                                                                              ctcCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGa                                                                                >  1:1583125/1‑94 (MQ=255)
                                                                                              ctcCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGa                                                                                <  2:1583125/94‑1 (MQ=255)
                                                                                              ctcCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATc                                            >  1:879188/1‑130 (MQ=255)
                                                                                              ctcCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATc                                            <  2:879188/130‑1 (MQ=255)
                                                                                               tcCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCAt                                                                                                          <  1:1036026/67‑1 (MQ=255)
                                                                                               tcCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCAt                                                                                                          >  2:1036026/1‑67 (MQ=255)
                                                                                                    tAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      >  1:892426/1‑114 (MQ=255)
                                                                                                    tAGGGACCAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      <  2:892426/114‑1 (MQ=255)
                                                                                                           cAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGaa                                                                                                                   >  1:1032330/1‑46 (MQ=255)
                                                                                                           cAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGaa                                                                                                                   <  2:1032330/46‑1 (MQ=255)
                                                                                                           cAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTggg                                                                                 >  2:30904/1‑80 (MQ=255)
                                                                                                           cAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTggg                                                                                 <  1:30904/80‑1 (MQ=255)
                                                                                                           cAGACCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCTGCTTTTAATAACGCTTCGCt                      >  1:1426124/1‑139 (MQ=255)
                                                                                                              aCCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTcgcg                                                        >  2:1328995/1‑102 (MQ=255)
                                                                                                              aCCTGCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTcgcg                                                        <  1:1328995/102‑1 (MQ=255)
                                                                                                                  gCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      >  1:856141/1‑100 (MQ=255)
                                                                                                                  gCCGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCa                                                      <  2:856141/100‑1 (MQ=255)
                                                                                                                    cGAAATCGGCAAATCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCTGCTTTTAATAACGCTTCGCTATCCCGAGc             <  2:1426124/139‑1 (MQ=255)
                                                                                                                              aaaTCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCTGCTTTTAATAACGCTTCGCTATCCCGAGCCAGCGTTGCa   <  2:784534/139‑1 (MQ=255)
                                                                                                                              aaaTCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCTGCTTTTAATAACGCTTCGCTATCCCGAGCCAGCGTTGCa   <  1:960662/139‑1 (MQ=255)
                                                                                                                              aaaTCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCTGCTTTTAATAACGCTTCGCTATCCCGAGCCAGCGTTGCa   <  2:1507979/139‑1 (MQ=255)
                                                                                                                               aaTCGCAATTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCAGCTTTTAATAACGCTTCGCTATCCCGAGCCAGCGTTGCAg  <  1:518911/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                  
TCTGGCTGGTAATACCCAGACTTGCGATCCATTTTTCCGGATCAAATTCACCAGCCTTATTGATATGTGCACTTCTTACCGCAACCATCGTCCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAACTATTTAACGCGCGAGAAAAGTACCATCGATTCCAGATGTCCCGTGTGTGGGAACATATCCAGCATCGCCAGTCGCGCAATGGTATATCCTGCTTTTAATAACGCTTCGCTATCCCGAGCCAGCGTTGCAG  >  NC_000913/2913564‑2913829

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A