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
A21 F59 I1 R1 23 54.9 2144786 90.8% 1947465 141.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase subunit beta

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,184,5430CA98.2% 164.2 / NA 56P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (31/22);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 4.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184404‑4184681
                                                                                                                                           |                                                                                                                                          
cTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGGCATCGTACTGAACCAGCt                                                                                                                                         >  1:217154/1‑143 (MQ=255)
  ggCGGTTAGACGCCGGAGCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAACTTCGAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                                       <  2:745528/143‑1 (MQ=255)
    cgggaaaaCGCCGTATCCAGCCCGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGc                                                                                                                                     <  1:130358/138‑1 (MQ=255)
       ttAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTa                                                                                                                                  >  1:808218/1‑143 (MQ=255)
             gCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGACCCAGCTGGGCGTACCGtct                                                                                                                            >  2:694340/1‑143 (MQ=255)
                 tATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTa                                                                                                                        <  2:555667/143‑1 (MQ=255)
                  agccAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                       <  1:450688/141‑1 (MQ=255)
                   tCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACAGAACCACCTGGGCGTACCGTCCCGTATg                                                                                                                      >  2:168460/1‑143 (MQ=255)
                    ctcggcTGGTGACGAGGTGGCAGGTCGGCGCGGTAACGAGGGTGTCATTTCTAAGGTCGACCCGATCGAAGATATGCCTTACGATGACAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGa                                                                                                                     <  2:659418/138‑1 (MQ=255)
                        ccTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGACCAt                                                                                                                 >  1:1038662/1‑143 (MQ=255)
                          tGGTGACAGGAGGGCAGCTGGGCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGAGCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCCCGTATGAACATCg                                                                                                               <  2:961518/143‑1 (MQ=255)
                             tggcAAGGTGGCAGGTCGTCACGGGAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTc                                                                                                            <  2:562113/140‑1 (MQ=255)
                             tGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGtg                                                                                                            >  2:905331/1‑142 (MQ=255)
                             tGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTc                                                                                                            >  1:821409/1‑143 (MQ=255)
                              gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                           >  2:553285/1‑143 (MQ=255)
                                cAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGGCAGa                                                                                                         >  1:361140/1‑143 (MQ=255)
                                 aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACCTCGTACTGAACCAGCTGGGCGTCGCGTCTCGTATGAACATCGGTTAGAt                                                                                                        >  1:255382/1‑143 (MQ=255)
                                 aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTATAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGACGGTAGACAGCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAGCATGGGGCGGAt                                                                                                        >  1:918946/1‑143 (MQ=255)
                                  aGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATc                                                                                                       <  2:343989/143‑1 (MQ=255)
                                     tGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCGGGGTTCAGCCCTATCGAAGATATGCCTTACGATTAAGACGTTACGCCAGTAGACATCGAACTGAACCAGCTGGGCGTACCGTCTCGTCAGAACATCGGTCAGAACCTc                                                                                                    >  2:707410/1‑143 (MQ=255)
                                      ggCAGGTCGTCACGGGAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCg                                                                                                   <  1:642535/143‑1 (MQ=255)
                                         aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                                >  1:648573/1‑143 (MQ=255)
                                                   ggTAACAAGGGTGTAATTTCTAAGATCAACCCGATAGAAGATATGCCTTACGATGAAAACGGTACGACGGTAGACATCGGACTGAACCAGCCGGGCGTAGTGTCCCGTATGAACATCGGTTAGATCCTGGAAAaccacccgag                                                                                      >  2:88316/1‑139 (MQ=255)
                                                            ggTGTAATCTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                             <  1:920854/143‑1 (MQ=255)
                                                                 aagttCGAAGATCAACCCGATCGAAGATATGCCCGACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                        <  1:760313/140‑1 (MQ=255)
                                                                 aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACAAGCTGGACGAAACGTCTCGAAAAAACATCGGACAAATCCTCGAAAACCCACAGAGTATGGATGcacaag                                                                        >  2:698517/1‑138 (MQ=255)
                                                                       tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                                  >  1:68089/1‑143 (MQ=255)
                                                                        aagcgcAACCCGATCGCAGAGATGCCTGACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCgg                                                                 <  2:392175/138‑1 (MQ=255)
                                                                        aaGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCgg                                                                 <  1:916391/143‑1 (MQ=255)
                                                                           aTCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTCCGAAAGGTACCGGCGa                                                              >  2:471596/1‑143 (MQ=255)
                                                                               gccggATCGAAGAGGTGCCTGACGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATTGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAg                                                          <  2:886622/139‑1 (MQ=255)
                                                                               aCCCGATCGAAGATATGCCTTACGATGAAGACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATTGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAg                                                          <  2:333574/143‑1 (MQ=255)
                                                                                  cGATCGACGATATGCCTGACGATGAAGACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGACGGAGACAACAATCTGCCTGCGAAAGGTATCGGCGACAAGATc                                                       <  2:78872/143‑1 (MQ=255)
                                                                                     tCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                       <  1:768960/108‑1 (MQ=255)
                                                                                     tCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                       >  2:768960/1‑108 (MQ=255)
                                                                                       gAAGATATGCCTTACGATGAGACCGGTACGCCGGTAGACATCGTACTGAACCTGCTGGGCGTACCGTCTCGTATGAACATCGGTGAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGc                                                  <  2:662046/143‑1 (MQ=255)
                                                                                       gAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGAGACAAGATCAACGc                                                  >  2:407969/1‑143 (MQ=255)
                                                                                           atatGTCTTACGATGAAAACGGTACGCCGGGAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCGTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATg                                              <  1:802551/143‑1 (MQ=255)
                                                                                           atatGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTATCGAAAGAACATCAGAAAGATAAAAGAAACCAACATGGGTATGGCTGCGAAAGGTAACGGCGACAAGATCAACGCCATg                                              >  1:10699/1‑143 (MQ=255)
                                                                                               gCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGa                                          >  2:564587/1‑143 (MQ=255)
                                                                                                ccTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaa                                         >  2:615480/1‑143 (MQ=255)
                                                                                                  ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGGACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACCAGATCAACGCCATGCTGAAAc                                       >  2:705341/1‑143 (MQ=255)
                                                                                                     cgacgaAGAGGGTACGCAGGTAGACTTCGTACTGAACCGGCTGGGGGTGCGCGGGCGCACAACCCTCGGTCATAGGCCCTAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcagc                                    <  2:758485/143‑1 (MQ=255)
                                                                                                      gATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTCTGGCTGCGAAAGGTAACGGCGACAAGATCAACGCCAAGCTGAAAcagca                                   >  1:134010/1‑143 (MQ=255)
                                                                                                           aaaCGTTACTCCGGTAGTCATCGTACTGAACCAGCTGGGGGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaag                              <  1:694340/143‑1 (MQ=255)
                                                                                                              cGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTCCCGCCTCATTTGGTTTCCTGTTAGATCACAATCTTTTATCTTTGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCCGAAACAGCAGCaagaag                           >  1:1066581/1‑143 (MQ=255)
                                                                                                                       ggTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCCGGGTATGGCTGCGCAAGGTATCGGCGACAACATCAACGCCATGCCGAAACAGCCGCAAGAAGTCGCGaacc                  >  1:746356/1‑141 (MQ=255)
                                                                                                                         tAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTg                <  1:649614/143‑1 (MQ=255)
                                                                                                                           gACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAACCAGCAGCAAGCAGTCGCGAAACTgcg              >  1:796479/1‑143 (MQ=255)
                                                                                                                               tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa          <  1:331899/143‑1 (MQ=255)
                                                                                                                               tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa          >  1:539111/1‑143 (MQ=255)
                                                                                                                               tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAAGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa          >  1:539088/1‑143 (MQ=255)
                                                                                                                                 gTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAtt        <  2:648573/143‑1 (MQ=255)
                                                                                                                                  tACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTc       <  1:642787/143‑1 (MQ=255)
                                                                                                                                     tGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATc    >  2:572512/1‑143 (MQ=255)
                                                                                                                                       aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCa  >  1:119264/1‑143 (MQ=255)
                                                                                                                                           |                                                                                                                                          
CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184404‑4184681

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A