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
A18 F36 I0 R1 2686 148.3 4982338 97.1% 4837850 149.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,708,758 G→C 20.0% E614Q (GAA→CAA)  rsxC → SoxR [2Fe‑2S] reducing system protein RsxC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,708,7580GC20.0% 17.1 / 3.8 20E614Q (GAA→CAA) rsxCSoxR [2Fe‑2S] reducing system protein RsxC
Reads supporting (aligned to +/- strand):  ref base G (6/8);  new base C (2/2);  total (9/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGA  >  NC_000913/1708612‑1708901
                                                                                                                                                  |                                                                                                                                               
gcgcCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCTCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAAc                                                                                                                                              <  2:1961341/150‑1 (MQ=255)
                  tGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCAGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCACAAAAGAAGCACCACCAAAAGGCTAATACGGAAAAAGAATAACAGGAAGATACGAGCAAAg                                                                                                                            >  2:2282650/1‑150 (MQ=11)
                         cctaCAGCCTAATGCGGAACCAGAACACCAGGGGGATCCCCGGAAAGCCGCCGTCGAAGCCGCTATGGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGt                                                                                                                     <  1:881336/147‑1 (MQ=14)
                                  tAATTCGGAACCCGAAGAACACGGCGATCCTCGCAAAGCTGCCGTTGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGTAACCAGAAGAACATGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGc                                                                                                            <  2:1959361/150‑1 (MQ=11)
                                  tAATTCGGAACCAGAACCACAGGTCGATCCTCGCAAACCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGc                                                                                                            <  2:1964450/150‑1 (MQ=255)
                                                                                    cagCTATCGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGAt                                                                                                                                      <  2:1061427/72‑1 (MQ=9)
                                                                                        catcgCCCGTGCCAATGCTCGCAAGCTTTAACAGCAACAGGCTAATGCGGAACCAGAATAACAGGTCGATCCGCGCAAAGCCGCCTTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGcc                                                      <  2:16548/146‑1 (MQ=11)
                                                                                           tGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCGGGAGCAGCGACCGGCGAATGCCGAGCCAgc                                                   >  1:1228620/1‑149 (MQ=11)
                                                                                            gCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGACCCAGAAGAACAGGTCGATCCGCGCAAAGCTGCCGTCGAAGCGGc                                                                                                            >  1:1234801/1‑92 (MQ=255)
                                                                                                    cAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATCCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCAGAGCCAGAACAagagat                                          >  2:929727/1‑148 (MQ=255)
                                                                                                             cAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTAGCAGCGGCTATTGCCCGAGCGCACGCCCGCAACCAGGACCAGCAGCAGGCTAAAGACGAGCCCGAACACGAGGTCgcaacccc                                 >  1:1152138/1‑143 (MQ=2)
                                                                                                                         gCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAg                                                                          <  1:646945/97‑1 (MQ=37)
                                                                                                                           aaCAGGCTAATCCGGAACCAGAACAACAGGCCGATCCCCGCAAACCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCg                   <  1:1918976/150‑1 (MQ=11)
                                                                                                                               ggCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAg                                                                                           <  2:1929638/74‑1 (MQ=34)
                                                                                                                                    aTGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGaac                                                 >  1:264466/1‑111 (MQ=37)
                                                                                                                                    aTGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGaac                                                 <  2:264466/111‑1 (MQ=37)
                                                                                                                                       cGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAg                                                    <  2:2426784/105‑1 (MQ=255)
                                                                                                                                       cGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAg                                                    >  1:2426784/1‑105 (MQ=25)
                                                                                                                                        ggAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCCCGCAAGCTGGACCAGCAACCGGCTAATGCCGAGCCAGAACCACAGGTCGATCCGCGCAAAGCAGCCGTCGAAGCCGCTATTGc      >  1:1205165/1‑150 (MQ=14)
                                                                                                                                            ccAGAAGAACAGGTCGATCCGCGCAAAGCCGCAGTAGAAGCAGCTATTGACCGAGACAAAGAACGAAAGCTGGAAAAGAAAAAGGCTAATGCCGAGCCAGAAGAACAGGTAGATACGCGCAAAGCGGCCGTCGAAGCCGCTAGTGCCCgc  >  2:928119/1‑149 (MQ=11)
                                                                                                                                                  |                                                                                                                                               
GCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGA  >  NC_000913/1708612‑1708901

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A