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
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,312,170 G→C 11.4% L194V (CTG→GTG)  ompC ← outer membrane porin protein C

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,312,1700GC11.4% 134.2 / 10.6 44L194V (CTG→GTG) ompCouter membrane porin protein C
Reads supporting (aligned to +/- strand):  ref base G (19/20);  new base C (2/3);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-02

GTAGGTTTCAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGA  >  NC_000913/2312024‑2312304
                                                                                                                                                  |                                                                                                                                      
gtAGGTTTCAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGt                                                                                                                                       >  4:934912/1‑148 (MQ=255)
gtAGGTTTCAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGt                                                                                                                                       >  4:248345/1‑148 (MQ=255)
 tAGGTTTCAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTg                                                                                                                                      <  3:934912/148‑1 (MQ=255)
 tAGGTTTCAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTg                                                                                                                                      <  3:248345/148‑1 (MQ=255)
     tttCAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTg                                                                                                                                      <  4:184147/144‑1 (MQ=255)
     tttCAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTg                                                                                                                                      >  3:184147/1‑144 (MQ=255)
        cAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCACTGCGTCaaa                                                                                                                               <  1:152948/148‑3 (MQ=255)
             cGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgt                                                                                                                          >  2:1125915/1‑148 (MQ=255)
                 cGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgttgtt                                                                                                                      <  3:640431/148‑1 (MQ=255)
                       tACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGCTAGAACCGCCGACGCCGTCGCCGTTTTGACGCAg                                                                                                                                        <  4:743081/124‑1 (MQ=255)
                       tACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAg                                                                                                                                        >  3:743081/1‑124 (MQ=255)
                         ccGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgttgtt                                                                                                                      >  4:740522/1‑140 (MQ=255)
                         ccGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgttgtt                                                                                                                      <  3:740522/140‑1 (MQ=255)
                              gTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgt                                                                                                                          >  4:615295/1‑131 (MQ=255)
                              gTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgt                                                                                                                          <  3:615295/131‑1 (MQ=255)
                               tAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgttg                                                                                                                        >  4:310214/1‑132 (MQ=255)
                               tAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgttg                                                                                                                        <  3:310214/132‑1 (MQ=255)
                                  gcagcGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTaa                                                                                                     <  1:1125915/148‑1 (MQ=255)
                                                    tCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCTTTTTGACGCAGTGCGTCACGACCgttg                                                                                                                        >  2:456216/1‑111 (MQ=255)
                                                    tCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgttg                                                                                                                        <  1:456216/111‑1 (MQ=255)
                                                     cAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgttgtt                                                                                                                      >  4:855191/1‑112 (MQ=255)
                                                     cAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCgttgtt                                                                                                                      <  3:855191/112‑1 (MQ=255)
                                                         aCGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCAc                                                                                            <  2:846610/134‑1 (MQ=255)
                                                         aCGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCAc                                                                                            >  1:846610/1‑134 (MQ=255)
                                                                gAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCACTGCGTCaaaa                                                                                                                              >  4:317503/1‑90 (MQ=255)
                                                                gAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCACTGCGTCaaaa                                                                                                                              <  3:317503/93‑4 (MQ=255)
                                                                    tGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGtt                                                                            <  1:634447/139‑1 (MQ=255)
                                                                    tGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGtt                                                                            >  2:634447/1‑139 (MQ=255)
                                                                                            aaCCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACt                                                                                                          >  4:933798/1‑85 (MQ=255)
                                                                                            aaCCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACt                                                                                                          <  3:933798/85‑1 (MQ=255)
                                                                                             aCCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGAAGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAATAAACCCTTCACCAGATTGGTTGCCGTTCTTACCCTGGTACTGAACAGCAAAGGTCTGGCCg                                          >  1:388345/1‑148 (MQ=255)
                                                                                                          tAAGTGATAGAACCGCCGACGCCGTCGCCGTTTAGACGGAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCga                             <  2:388345/148‑1 (MQ=255)
                                                                                                           aaGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCaa                                                     <  2:852707/123‑1 (MQ=255)
                                                                                                           aaGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCaa                                                     >  1:852707/1‑123 (MQ=255)
                                                                                                                        gccgACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATg                                                                                      <  1:56464/77‑1 (MQ=255)
                                                                                                                        gccgACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATg                                                                                      >  2:56464/1‑77 (MQ=255)
                                                                                                                                     ccgtTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCt                                                                    >  2:17347/1‑82 (MQ=255)
                                                                                                                                     ccgtTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCt                                                                    <  1:17347/82‑1 (MQ=255)
                                                                                                                                         tttGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGa  >  4:528338/1‑144 (MQ=255)
                                                                                                                                         tttGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGa  <  3:528338/144‑1 (MQ=255)
                                                                                                                                           tGACGCACTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAAc                                                          <  3:929676/86‑1 (MQ=255)
                                                                                                                                           tGACGCACTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAAc                                                          >  4:929676/1‑86 (MQ=255)
                                                                                                                                               gCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc                      <  1:72491/118‑1 (MQ=255)
                                                                                                                                               gCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc                      >  2:72491/1‑118 (MQ=255)
                                                                                                                                                cAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCaa                                      >  1:307357/1‑101 (MQ=255)
                                                                                                                                                cAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATCGGTTGCCGTTTTTTCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCaa                                      <  2:307357/101‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                      
GTAGGTTTCAGCACGGTCGCCGTTACCGATGTAAGCAGCGGTGTTCTGAGCATCAGTACGTTTGGAGCTGGAGATCGCACCACCGATACCGAAACCTTCGTAATCATAAGTGATAGAACCGCCGACGCCGTCGCCGTTTTGACGCAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGA  >  NC_000913/2312024‑2312304

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A