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 F14 I0 R1 206 76.7 3255580 98.8% 3216513 146.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 4,158,463 C→G 27.3% A158G (GCG→GGG)  PP_3661 → membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC4,158,4630CG27.3% 38.0 / 2.9 32A158G (GCG→GGG) PP_3661membrane protein
Reads supporting (aligned to +/- strand):  ref base C (8/15);  new base G (6/3);  total (14/18)
Fisher's exact test for biased strand distribution p-value = 1.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATG  >  NC_002947_CJ‑RC/4158323‑4158584
                                                                                                                                            |                                                                                                                         
ggTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGCATCGGGGCGgcgcc                                                                                                                   >  4:123247/1‑148 (MQ=255)
             aCCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGGCGCGcccccccca                                                                                                       >  1:69331/1‑145 (MQ=255)
               cAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCAaaaa                                                                                                     >  1:310913/1‑148 (MQ=255)
                 gTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGAGCCCCGCCCCCCCAaaaaa                                                                                                   >  2:349916/1‑147 (MQ=255)
                 gTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCCCGCCCCCCCCaaaaac                                                                                                  >  3:326203/1‑147 (MQ=255)
                  tACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCTGCGCCGCGCCCCCCCAAAAAacg                                                                                                 >  2:287770/1‑149 (MQ=255)
                  tACCCGGCTGATCGGCCTGTGGTGTGGCATAAAATTTTCCAAGCTCGCCCGCTAAACCGCCTTGCTCACCGCCGCCGGCAGCGCAATCTGCGGCGCCGCCGCCGGGCTGCAATTCGAATCGGCGCTGCGCAGCGCCTCCCATAAAAgc                                                                                                  <  2:198420/148‑1 (MQ=255)
                       tgctgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCCCCCCCCCCaaaaaaaacccaa                                                                                             >  5:159700/1‑141 (MQ=255)
                             tCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCGCGCCCCCCAAAAAAGCGCCCTGGCAGt                                                                                       >  6:332979/1‑148 (MQ=255)
                                 ccTGGGGGGTGGCATTAATGTGTTCACGCGCGCCCGCGAACCCGCCTTGCTGCCCGCCGCGGGCAGCGCCTTCTGCGGCGCCGCCGCCGTGCTGGCATTCTAATCGGCGCTGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGaa                                                                                  <  4:326203/149‑1 (MQ=255)
                                   tgtggtgtggCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCGCGCCCCCCCCAAAAGCCCCAAGGCAGTGGGCAg                                                                                 >  5:196544/1‑148 (MQ=255)
                                            gCATGAATTTGTTCAAGCTCGACCGCTATACCGCCTTGCTTACCGCCGCCGTCTGCGCCAGCTGGGGCGCCGCCGCGGTTGTGGCATTCGACTCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCt                                                                        <  2:237762/148‑1 (MQ=255)
                                             aaTGAAAGTGTTCATGCTCGACCGCTATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGGGCGGGAATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGt                                                                      <  4:28915/148‑1 (MQ=255)
                                                 aaaGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGGGCCGCCACGGTGGGGGATTTCTAATCGGGGCTGGGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCg                                                                   <  8:294006/148‑1 (MQ=255)
                                                               cGACCGCGATACTGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCACCGCCCCCCAGAAAAGCGCCAAGGCCGTCGGAAGCGGAGTGGTGTTCGGTGCCTTGGCGATg                                                     >  8:411440/1‑148 (MQ=255)
                                                               cGACCGCGATACCGCCTTGCTGCCCGCCGCCGGCCGCGCCATCTGCGGCGCCGCCGCGGTGCTGGCATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATg                                                     <  6:234661/148‑1 (MQ=255)
                                                                  ccGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCTGCGCAGCGCCCCCCAAAAAAACGCCAAAGCAGTACGAATCCTAGAGCAGTTAGGTAACATGTGGAtttt                                                   >  6:302859/1‑147 (MQ=255)
                                                                           cGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCTCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCAc                                        <  2:264949/149‑1 (MQ=255)
                                                                             ccTTGCTCCCCCCCCCCGCCCGCGCCAGCGGCGGCGCCGCCGCGGGGCTGCAATTCCACGCGGCGCGGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACt                                       <  6:144398/148‑1 (MQ=255)
                                                                                  cTGCCCGCCGCGGGCTGCGCCATCGGGGGCGCCGCCGCGGTGGTGGCTTTCTATGCGGCGGGGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGa                                  <  6:24346/148‑1 (MQ=255)
                                                                                   tGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGCGCCGCGCCCCCCCAAAAAACGCCCAGGGAGTGGGGAGGGGAGTGGGGTTGGGTTGCGTGTGGGTGTTGGTTTTCCCACAgggggt                                 >  2:9500/1‑144 (MQ=255)
                                                                                      ccgccgccgGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGCGCCCCGCCCCCCCAAAAAACGCCCTGGCAGTCGGAAGCGGAGTGGTGTTGGGGAACGTGTGGTAGTTGGTTTTACCACAGGCGAtga                               >  8:358929/1‑145 (MQ=255)
                                                                                            ccgGCCGCGCCTTCGGGGGCGCCGCCGCGGTGCTGTCATTCTACTGGGGGCTGCCCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggc                       <  1:349916/149‑1 (MQ=255)
                                                                                                 aGCGCCATCTGCGGCGCCGGCGCCGGGCTGGAATTGGACTGGGCGGGGGGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggctggct                  <  4:212566/149‑1 (MQ=255)
                                                                                                 aGCGCCATCTGCGGCGCCGCCGCCGTCCCGCCATTCGAATCGCCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGCCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggctggct                  <  2:310913/149‑1 (MQ=255)
                                                                                                    gcCCTCGGCGGCGCCGCCGGCGTGCTTGATTGCCTCGCGGGGGGGCGCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTGCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCa               <  3:109966/149‑1 (MQ=255)
                                                                                                     ccATGTGCGGCGCCGCCGCGGGGCTGGCATTCGAAGCGGCGCGGCGAAGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCAt              <  4:240142/149‑1 (MQ=255)
                                                                                                         gggcggcgCCGCCGCGGTGCTGTAATTCTATGCGGCGCTGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTg           <  2:73326/146‑1 (MQ=255)
                                                                                                         cggcggcgCCGCCGGCGTGGGGGAATTCGACGCGGCGCGGCGCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTg           <  5:258989/146‑1 (MQ=255)
                                                                                                          ggcggcgCCGCCGCCGGGCTGCCATTCGACGCGGCGCGGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGa         <  3:336309/148‑1 (MQ=255)
                                                                                                                 ccgccgcggGGGTGGAATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATg  <  2:69331/149‑1 (MQ=255)
                                                                                                                                        tCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGGAGTGCTGTTAGGTACCTTGTCGATGTTGCTTTAACCACTGGCGATCAATTCCg                         >  7:247247/1‑103 (MQ=255)
                                                                                                                                            |                                                                                                                         
GGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATG  >  NC_002947_CJ‑RC/4158323‑4158584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A