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
A2 F1 I1 R1 404 265.1 10478538 96.8% 10143224 150.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP009974 4,543,833 C→G S430S (TCG→TCC)  RPPX_20290 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0099744,543,8330CG94.9% 55.7 / ‑1.0 39S430S (TCG→TCC) RPPX_20290hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base G (18/19);  total (20/19)
Fisher's exact test for biased strand distribution p-value = 4.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

CTGCCGCTGCGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAAGCCGTCTTGAGCGATAGGATGTTGAACCACAGCATCCCCGCGTTTAAACCACCACCACCGCCCGAGGTGAGCAACCCAAGGAAGTTGGGTTTCACACGCGCAGTGGTGGTCAGCTCGATAGACACCGTGCGGCTACCCGAGATGCGCAACGCTTTCATCTCTTCAACCTGTGCCATGCCGCTCTTCAAATACCGCTGCACCTCCTGGCT  >  CP009974/4543685‑4543979
                                                                                                                                                    |                                                                                                                                                  
gtgccggtgcGCCAATCACACCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGa                                                                                                                                                  <  2:2903229/150‑1 (MQ=11)
ctgccgctgcGCCAATCACCCCGATCACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGa                                                                                                                                                  <  2:4877333/151‑1 (MQ=11)
ctgccgctgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGa                                                                                                                                                  >  2:4612694/1‑151 (MQ=11)
   cctctgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGt                                                                                                                                               >  1:1366444/4‑151 (MQ=11)
   ccgctgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGt                                                                                                                                               <  1:4719877/151‑1 (MQ=11)
    cgctgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTg                                                                                                                                              <  1:2694689/151‑1 (MQ=11)
     gctgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGa                                                                                                                                             >  1:2533311/1‑151 (MQ=11)
     gctgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGa                                                                                                                                             >  2:2798854/1‑151 (MQ=11)
     gctgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGa                                                                                                                                             <  1:363504/151‑1 (MQ=11)
      ctgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAg                                                                                                                                            >  2:1596546/1‑151 (MQ=11)
       tgcGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGc                                                                                                                                           >  2:2263460/1‑151 (MQ=11)
        gcgcCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCa                                                                                                                                          >  2:1110304/1‑151 (MQ=11)
         cgcCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCaa                                                                                                                                         >  2:1447897/1‑151 (MQ=11)
          gcCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAAc                                                                                                                                        <  2:3477675/151‑1 (MQ=11)
          gcCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAAc                                                                                                                                        >  2:4170573/1‑151 (MQ=11)
            cAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAAccc                                                                                                                                      <  2:288247/151‑1 (MQ=11)
            cAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAAccc                                                                                                                                      <  1:1140695/151‑1 (MQ=11)
            cAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAAccc                                                                                                                                      >  2:2612354/1‑151 (MQ=11)
            cAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAAccc                                                                                                                                      <  2:1155416/151‑1 (MQ=11)
            cAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAAccc                                                                                                                                      >  1:2862074/1‑151 (MQ=11)
               tCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAg                                                                                                                                   <  1:1564266/151‑1 (MQ=11)
               tCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAg                                                                                                                                   >  1:1342714/1‑151 (MQ=11)
               tCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAg                                                                                                                                   >  1:1341313/1‑151 (MQ=255)
                  ccccGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGaa                                                                                                                                >  2:2127722/1‑151 (MQ=11)
                  ccccGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGaa                                                                                                                                <  1:3308272/151‑1 (MQ=11)
                  ccccGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGaa                                                                                                                                <  1:2936673/151‑1 (MQ=11)
                    ccGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGt                                                                                                                              <  2:3688251/151‑1 (MQ=11)
                     cGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGATGTGAGCAACCCAAGGAAGtt                                                                                                                             >  2:539838/1‑151 (MQ=11)
                     cGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGtt                                                                                                                             <  1:3737429/151‑1 (MQ=11)
                     cGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGtt                                                                                                                             <  1:3547360/151‑1 (MQ=11)
                     cGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGtt                                                                                                                             >  1:2551002/1‑151 (MQ=11)
                      gAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGTTg                                                                                                                            <  2:81181/151‑1 (MQ=11)
                      gAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGTTg                                                                                                                            >  1:5138710/1‑151 (MQ=11)
                      gAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGTTg                                                                                                                            >  1:434346/1‑151 (MQ=11)
                       aaCACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGTTgg                                                                                                                           <  1:1068993/151‑1 (MQ=11)
                        acacAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGTTggg                                                                                                                          <  1:1169689/151‑1 (MQ=11)
                         cacaGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAGGCCGTGTTGAGCGATAAGATGTTGAACCACAGCATCCCTGCGTTTAAACCACCACCACCGCCGGAGGTGAGCAACCCAAGGAAGTTGGGt                                                                                                                         <  2:719422/151‑1 (MQ=11)
                                                                                                                                           cccaccGCCCGAGGTGAGCAACCCAAGGAAGTCGGGTTTCACACGCGCAGTGGTGGCCAGCTCGATAGACACCGTGCGGCTACCCGAGATGCGCAACGCTTTCATCTCTTCAACCTGCGCCATGCCCCTCTTCAAATACCGCTGCAcctcc       >  2:4743803/2‑151 (MQ=2)
                                                                                                                                                cGCCCGAGGTGAGCAACCCAAGGAAGTTGGGTTTCACACGCGCAGTGGTGGTCAGCTCGATAGACACCGTGCGGCTACCCGAGATGCGCAACGCTTTCATCTCTTCACCCTGCGCCACGCCGCTCTCCAACTACCGCCGCACCTCCTCGcc  >  2:4116088/1‑150 (MQ=11)
                                                                                                                                                    |                                                                                                                                                  
CTGCCGCTGCGCCAATCACCCCGAACACAGATGAAGCGAACCCCAGGGTGTATTCCGGTGCGTCGCTCTTCTGCAGGCTGTTGTAAGCCGTCTTGAGCGATAGGATGTTGAACCACAGCATCCCCGCGTTTAAACCACCACCACCGCCCGAGGTGAGCAACCCAAGGAAGTTGGGTTTCACACGCGCAGTGGTGGTCAGCTCGATAGACACCGTGCGGCTACCCGAGATGCGCAACGCTTTCATCTCTTCAACCTGTGCCATGCCGCTCTTCAAATACCGCTGCACCTCCTGGCT  >  CP009974/4543685‑4543979

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A