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
A5 F28 I1 R1 157 47.3 1607120 99.4% 1597477 138.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,024,384 G→A intergenic (‑36/‑87) yccF ← / → helD conserved inner membrane protein YccF/DNA helicase IV

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,024,3840GA100.0% 205.6 / NA 58intergenic (‑36/‑87)yccF/helDconserved inner membrane protein YccF/DNA helicase IV
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/31);  total (27/31)

ATCAGCACAATACTGACCAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCGGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGCACAGCACCCT  >  NC_000913/1024254‑1024518
                                                                                                                                  |                                                                                                                                      
aTCAGCACAATACTGACCAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTa                                                                                                                               >  2:367950/1‑140 (MQ=255)
   aGCACAATACTGACCAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACg                                                                                                                            >  2:383334/1‑140 (MQ=255)
    gCACAATACTGACCAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGt                                                                                                                           >  2:622473/1‑140 (MQ=255)
      acaATACTGACCAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGttt                                                                                                                         <  2:703931/140‑1 (MQ=255)
             tGACCAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTggg                                                                                                                  <  2:58964/140‑1 (MQ=255)
               aCCAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCt                                                                                                                >  2:619796/1‑140 (MQ=255)
               aCCAGAGACGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGCTTTTTTGGGCt                                                                                                                >  1:498319/1‑140 (MQ=255)
                 cAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTgg                                                                                                              <  1:287774/140‑1 (MQ=255)
                    agTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGc                                                                                                           >  1:770957/1‑140 (MQ=255)
                    agTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGc                                                                                                           >  2:494787/1‑140 (MQ=255)
                    agTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGc                                                                                                           >  2:546341/1‑140 (MQ=255)
                    agTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGc                                                                                                           >  2:600988/1‑140 (MQ=255)
                    agTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGc                                                                                                           >  1:304245/1‑140 (MQ=255)
                    agTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGG‑TTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCa                                                                                                          >  2:224726/1‑140 (MQ=255)
                      tCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCAc                                                                                                         >  1:545528/1‑140 (MQ=255)
                       cGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACg                                                                                                        <  2:304245/140‑1 (MQ=255)
                         ccAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACg                                                                                                        <  1:363708/138‑1 (MQ=255)
                         ccAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACg                                                                                                        >  2:363708/1‑138 (MQ=255)
                               gccagccCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTctct                                                                                                <  1:14615/140‑1 (MQ=255)
                               gccagccCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTctct                                                                                                <  2:545528/140‑1 (MQ=255)
                               gccagccCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTctct                                                                                                <  1:206822/140‑1 (MQ=255)
                                ccagccCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTg                                                                                               <  1:383334/140‑1 (MQ=255)
                                 cagccCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGa                                                                                              <  1:546341/140‑1 (MQ=255)
                                    cccAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTctct                                                                                                >  2:623162/1‑135 (MQ=255)
                                    cccAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTctct                                                                                                <  1:623162/135‑1 (MQ=255)
                                     ccAGAGTGGTGGCAAATCCGCCAAGCGCAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCCCGTATTCTCTGACgat                                                                                          <  2:1404/140‑3 (MQ=255)
                                        gagTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTac                                                                                       >  1:92775/1‑140 (MQ=255)
                                         agTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTa                                                                                        <  2:131324/138‑1 (MQ=255)
                                         agTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTa                                                                                        >  1:131324/1‑138 (MQ=255)
                                              tggCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTaca                                                                                      >  1:260390/1‑135 (MQ=255)
                                              tggCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTaca                                                                                      >  1:305475/1‑135 (MQ=255)
                                              tggCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTaca                                                                                      <  2:260390/135‑1 (MQ=255)
                                              tggCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTaca                                                                                      <  2:305475/135‑1 (MQ=255)
                                              tggCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGAt                                                                                 >  1:602728/1‑140 (MQ=255)
                                               ggCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATa                                                                                <  1:619796/140‑1 (MQ=255)
                                               ggCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATa                                                                                <  2:349916/140‑1 (MQ=255)
                                                              cacaAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCgtg                                                                 <  2:770957/140‑1 (MQ=255)
                                                              cacaAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCgtg                                                                 <  1:600988/140‑1 (MQ=255)
                                                              cacaAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCgtg                                                                 <  1:622473/140‑1 (MQ=255)
                                                                caAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGtgtg                                                               <  1:494787/140‑1 (MQ=255)
                                                                       cAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTAc                                                        <  2:92775/140‑1 (MQ=255)
                                                                         gAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACag                                                      <  1:53454/140‑1 (MQ=255)
                                                                               tCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCAt                                                >  2:288783/1‑140 (MQ=255)
                                                                               tCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCAt                                                >  1:308548/1‑140 (MQ=255)
                                                                                   aaCGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGaa                                            <  2:753071/140‑1 (MQ=255)
                                                                                               aaaaCCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACa                                >  2:140004/1‑140 (MQ=255)
                                                                                                aaaCCTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACaa                               <  1:367950/140‑1 (MQ=255)
                                                                                                    cTCGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCt                           <  1:79181/140‑1 (MQ=255)
                                                                                                      cGCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTg                         >  1:195928/1‑140 (MQ=255)
                                                                                                       gCTTTACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTgg                        >  1:373886/1‑140 (MQ=255)
                                                                                                          ttACTGTGGTTTTCAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGaaa                     <  2:602728/140‑1 (MQ=255)
                                                                                                                       cAGTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGCACAg        <  1:288783/140‑1 (MQ=255)
                                                                                                                         gTAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGCACAGCa      <  2:197180/140‑1 (MQ=255)
                                                                                                                          tAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGca           >  2:513946/1‑134 (MQ=255)
                                                                                                                          tAATGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGca           <  1:513946/134‑1 (MQ=255)
                                                                                                                             tGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGca           >  1:628614/1‑131 (MQ=255)
                                                                                                                             tGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGca           <  2:628614/131‑1 (MQ=255)
                                                                                                                             tGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGCACAGCACCCt  >  2:172443/1‑140 (MQ=255)
                                                                                                                             tGGGCAGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGCACAGCACCCt  >  2:209439/1‑140 (MQ=255)
                                                                                                                               ggcagcAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGCACAg        <  1:79393/132‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                      
ATCAGCACAATACTGACCAGAGTCGCCAACAGCCAGCCCAGAGTGGTGGCAAATCCGCCAAGCACAAAGTTCAGAATGTTCAAAACGGTACGCATAAAACCTCGCTTTACTGTGGTTTTCAGTAATGGGCGGCAATTGTAACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGGTTACACTGATAAGAAATAATTTCGTGTGGATCTACAGAGTCATGGAACTGAAAGCGACAACGCTTGGAAAACGTCTGGCACAGCACCCT  >  NC_000913/1024254‑1024518

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