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
A9 F28 I1 R1 120 56.0 1898522 99.4% 1887130 138.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,979,911 G→A M53I (ATG→ATA)  uspC → universal stress protein C

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,979,9110GA98.1% 174.8 / ‑4.8 52M53I (ATG→ATA) uspCuniversal stress protein C
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (17/34);  total (17/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

CGCTGTTGCGGTTACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATGCTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACATATTCTGGAA  >  NC_000913/1979776‑1980040
                                                                                                                                       |                                                                                                                                 
cGCTGTTGCGGTTACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTg                                                                                                                               <  2:84878/140‑1 (MQ=255)
   tGTTGCGGTTACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAg                                                                                                                            >  2:805008/1‑140 (MQ=255)
        cGGTTACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTa                                                                                                                       >  1:9864/1‑140 (MQ=255)
          gTTACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACg                                                                                                                     >  1:29405/1‑140 (MQ=255)
          gTTACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACg                                                                                                                     <  1:940112/140‑1 (MQ=255)
           ttACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGc                                                                                                                    <  1:389589/140‑1 (MQ=255)
            tACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCa                                                                                                                   <  2:566575/140‑1 (MQ=255)
            tACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCa                                                                                                                   <  1:528527/140‑1 (MQ=255)
             acacCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAg                                                                                                                  <  2:293600/140‑1 (MQ=255)
               acCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCg                                                                                                                <  1:408186/140‑1 (MQ=255)
                ccGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATGCTTGAAGATTTACGCAGCGt                                                                                                               <  1:918619/140‑1 (MQ=255)
                ccGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGt                                                                                                               <  2:415953/140‑1 (MQ=255)
                 cGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTg                                                                                                              <  1:801345/140‑1 (MQ=255)
                 cGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTg                                                                                                              <  2:558296/140‑1 (MQ=255)
                 cGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTg                                                                                                              <  1:805008/140‑1 (MQ=255)
                   gAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCa                                                                                                                   <  2:240782/133‑1 (MQ=255)
                   gAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCa                                                                                                                   >  1:240782/1‑133 (MQ=255)
                                         aaGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCttt                                                                                      <  2:584797/140‑1 (MQ=255)
                                              gTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGa                                                                                 <  1:808398/140‑1 (MQ=255)
                                               tatctatcGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGAt                                                                                <  1:321922/140‑1 (MQ=255)
                                                    atcGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCtt                                                                                   <  2:685621/132‑1 (MQ=255)
                                                    atcGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCtt                                                                                   >  1:685621/1‑132 (MQ=255)
                                                    atcGCCAGGCCAGTAAAGGAACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGtt                                                                           <  2:399495/140‑1 (MQ=255)
                                                           ggccagTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAg                                                                    >  1:639113/1‑140 (MQ=255)
                                                              cagTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGAt                                                                 <  2:307607/140‑1 (MQ=255)
                                                              cagTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGAt                                                                 <  2:14168/140‑1 (MQ=255)
                                                              cagTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGAt                                                                 <  2:833094/140‑1 (MQ=255)
                                                               agTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATg                                                                >  1:52744/1‑140 (MQ=255)
                                                                 tAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCg                                                              <  2:52744/140‑1 (MQ=255)
                                                                   aaGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCggg                                                            <  2:345639/140‑1 (MQ=255)
                                                                                          tctcGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTa                                     <  1:472026/140‑1 (MQ=255)
                                                                                           ctcGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTAt                                    <  2:777355/140‑1 (MQ=255)
                                                                                              gCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGAc                                               >  1:482462/1‑126 (MQ=255)
                                                                                              gCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGAc                                               <  2:482462/126‑1 (MQ=255)
                                                                                              gCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGc                                 <  2:550087/140‑1 (MQ=255)
                                                                                                  ccGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGc                                 >  2:634943/1‑136 (MQ=255)
                                                                                                  ccGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGc                                 <  1:634943/136‑1 (MQ=255)
                                                                                                  ccGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTAc                             <  2:9864/140‑1 (MQ=255)
                                                                                                   cGACCCGGAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACg                            >  1:135671/1‑140 (MQ=255)
                                                                                                         ggAAATGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGt                      <  1:260498/140‑1 (MQ=255)
                                                                                                             aTGTACAATCAATTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAg                  <  2:135671/140‑1 (MQ=255)
                                                                                                                     tcaatTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACata          >  2:203629/1‑140 (MQ=255)
                                                                                                                     tcaatTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACata          >  2:142166/1‑140 (MQ=255)
                                                                                                                        atTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAAc             <  2:708845/134‑1 (MQ=255)
                                                                                                                        atTAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAAc             >  1:708845/1‑134 (MQ=255)
                                                                                                                         ttAGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACATATTCt      >  2:23650/1‑140 (MQ=255)
                                                                                                                           aGCTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACATATTCTgg    <  2:129365/140‑1 (MQ=255)
                                                                                                                             cTGCGCCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACATATTCTGGaa  >  2:188099/1‑140 (MQ=255)
                                                                                                                               gcgcCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACa            <  2:125944/128‑1 (MQ=255)
                                                                                                                               gcgcCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACa            >  1:125944/1‑128 (MQ=255)
                                                                                                                               gcgcCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACATATTc       >  1:828436/1‑133 (MQ=255)
                                                                                                                               gcgcCGATACTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACATATTc       <  2:828436/133‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                 
CGCTGTTGCGGTTACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTATCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGTACAATCAATTAGCTGCGCCGATGCTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGCAAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTGCCTACGGTGAGTTAAGCGAACATATTCTGGAA  >  NC_000913/1979776‑1980040

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