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
A3 F28 I1 R1 146 75.3 2562504 98.6% 2526628 139.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,942,117 G→A noncoding (310/1542 nt) rrsC → 16S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,942,1170GA78.0% 38.7 / 20.2 41noncoding (310/1542 nt)rrsC16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base G (5/4);  new base A (15/17);  total (20/21)
Fisher's exact test for biased strand distribution p-value = 7.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.63e-01

TACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGG  >  NC_000913/3941980‑3942168
                                                                                                                                         |                                                   
tACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGTGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAAcc                                                   >  2:315548/1‑140 (MQ=17)
 aCCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGaccaacca                                                  >  2:535502/1‑140 (MQ=17)
   cGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCcaca                                                >  1:911426/1‑140 (MQ=32)
   cGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCcaca                                                >  2:71259/1‑140 (MQ=32)
     cATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACt                                              >  1:398812/1‑140 (MQ=17)
     cATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACt                                              >  2:1131014/1‑140 (MQ=17)
     cATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACt                                              >  2:1196020/1‑140 (MQ=17)
     cATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACt                                              >  1:467944/1‑140 (MQ=17)
     cATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACt                                              >  1:357350/1‑140 (MQ=17)
     cATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACt                                              >  1:1157367/1‑140 (MQ=17)
     cATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATCAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACt                                              >  2:431425/1‑140 (MQ=17)
      aTAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTg                                             >  1:51931/1‑140 (MQ=17)
       tAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTgg                                            <  2:970573/140‑1 (MQ=17)
          cGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAAc                                         >  1:792245/1‑140 (MQ=17)
             cGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTga                                      >  1:532364/1‑140 (MQ=17)
                 aGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGaca                                  <  2:266367/140‑1 (MQ=32)
                 aGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGaca                                  <  2:911426/140‑1 (MQ=32)
                 aGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGaca                                  <  2:398812/140‑1 (MQ=17)
                 aGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGaca                                  <  2:978612/140‑1 (MQ=17)
                 aGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGaca                                  <  2:56610/140‑1 (MQ=17)
                     cAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGt                              >  2:1402/1‑140 (MQ=17)
                        agagGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCa                           <  2:481180/140‑1 (MQ=17)
                          agGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGa                         <  1:1402/140‑1 (MQ=17)
                             gggACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTc                      >  2:1222336/1‑140 (MQ=18)
                              ggACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTcc                     >  2:616077/1‑140 (MQ=17)
                               gACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCt                    >  1:1069281/1‑140 (MQ=33)
                                  cTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACg                 >  1:850932/1‑140 (MQ=33)
                                  cTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACg                 <  1:490264/140‑1 (MQ=17)
                                  cTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACg                 >  1:1117435/1‑140 (MQ=18)
                                    tCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACggg               >  1:359834/1‑140 (MQ=18)
                                       ggCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAgg            <  2:467184/140‑1 (MQ=32)
                                       ggCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAgg            <  2:357350/140‑1 (MQ=17)
                                          ctctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGgcag         <  1:1020775/140‑1 (MQ=17)
                                          ctctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACCATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGgcag         <  2:792245/140‑1 (MQ=17)
                                            ctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGgcagca       <  2:532364/140‑1 (MQ=17)
                                            ctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGgcagca       <  2:467944/140‑1 (MQ=17)
                                            ctTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGgcagca       <  1:1262717/140‑1 (MQ=17)
                                            ctTGCCATCAGATGTGCCCAGATGGGATCAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGgcagca       <  1:431425/140‑1 (MQ=17)
                                                 cATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGTGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTggg  <  1:315548/140‑1 (MQ=12)
                                                 cATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTggg  <  1:1222336/140‑1 (MQ=17)
                                                 cATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTggg  <  1:582857/140‑1 (MQ=17)
                                                 cATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAACCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTggg  <  1:957499/140‑1 (MQ=17)
                                                                                                                                         |                                                   
TACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGG  >  NC_000913/3941980‑3942168

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