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 F13 I0 R1 203 85.6 3649704 98.8% 3605907 146.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 4,158,466 T→G 60.7% L159R (CTG→CGG)  PP_3661 → membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC4,158,4660TG60.7% 2.6 / 17.1 35L159R (CTG→CGG) PP_3661membrane protein
Reads supporting (aligned to +/- strand):  ref base T (4/10);  new base G (10/10);  total (15/20)
Fisher's exact test for biased strand distribution p-value = 2.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.61e-01

CGGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCA  >  NC_002947_CJ‑RC/4158322‑4158609
                                                                                                                                                |                                                                                                                                                  
cGGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTgc‑g‑c                                                                                                                                              <  1:327585/149‑1 (MQ=255)
 ggTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGACATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGC‑G‑C‑a                                                                                                                                            <  5:287643/149‑1 (MQ=255)
  gTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTAC‑G‑C‑Ag                                                                                                                                           <  3:110888/149‑1 (MQ=255)
              aCCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCACTGC‑G‑C‑AGCGCCCCCCATa                                                                                                                                >  7:195729/1‑148 (MQ=255)
              aCCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGGGCTGGCATTCGACTCGGGGGGGC‑G‑C‑CGCGCCCCCCCTa                                                                                                                                >  4:19716/1‑148 (MQ=255)
                cAGTACCGTGCTGAGCGGCCTGTGGTGGGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGCCCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCTAATCGGCGCTGC‑G‑C‑AGCGCCCCCCATaaaa                                                                                                                             <  4:32186/149‑1 (MQ=255)
                cAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGC‑G‑G‑CGCGCCCCCCAaaaa                                                                                                                              >  6:133426/1‑148 (MQ=255)
                      ccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGCGG‑C‑CCCCCCCCCCaaaaaacccc                                                                                                                         >  7:320071/1‑144 (MQ=255)
                      ccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGG‑GCCGC‑G‑CGCGCGCCCCCCCCaaaaacaaca                                                                                                                       >  7:237730/1‑143 (MQ=255)
                         gctgtggggCCGGTGGTGGGGCATTAATGTGTTCACGCCCCCCCGCTATCCCGCCTTGCTCCCCGCCCCCGCCCGCGCCATCGGCGGCGCCGCCGCGGTGCTGCATTTCTAATCGGCGCGGC‑G‑C‑CGCGCCCCCCATAAAAGCGCCATgg                                                                                                                    <  8:345130/142‑1 (MQ=255)
                          ctgATCGGCCTGTGGTGTGGCTTTAATGTGTTCAAGCTCGACCGCTATACCGCCTTGCTCACCGCCGCGGGCTGCGCCATCTGGGGCGCCGCCGCCGTGGTGGCATTCTAAGCGGCGCTGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATgg                                                                                                                    <  6:375808/148‑1 (MQ=255)
                                          gtggCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGGGGG‑G‑G‑CGCGCCCCCCCAAAAAACCCCAAGGCCCTCGGGAGCGGAGTg                                                                                                   >  7:70474/1‑149 (MQ=255)
                                          gtggCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGC‑G‑C‑CGCGCCCCCCCAAAAAGCGCCCAGGCAGTCGGGAGCGTAGTg                                                                                                   >  6:140342/1‑149 (MQ=255)
                                             gCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGGGGC‑C‑C‑AGCGCCCCCCCAAAAAACGCCAAAGGAGACGGAAACCGAGTGCTg                                                                                                >  4:120016/1‑149 (MQ=255)
                                             gCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGC‑G‑C‑AGCGCCCCCCCAAAAAACCCCAAGGCAGTCGGAAGCGTAGTGCTg                                                                                                >  8:155936/1‑149 (MQ=255)
                                             gCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCACCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGG‑G‑C‑CGCGCCCCCCCAAAAAGCGCCATGGCAGGCGGAAGCGTAgtggtg                                                                                                >  5:103754/1‑149 (MQ=255)
                                               aTGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGC‑G‑C‑ACCGCCCCCCCAAAAAACGCCAAGGCAGTCGGAAGCGTAGTGGTGtt                                                                                              >  2:296353/1‑149 (MQ=255)
                                                          cAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGC‑G‑C‑AGCGCCCCCCCCAAAACCGCCAACGCAGGGGGAAGCGGAGTGGTGGTGGGGAGCTTGt                                                                                   >  1:259696/1‑149 (MQ=255)
                                                           atcgtCGTCCGCGATACCCCCTGGTTGCCCGGCCCCGTCAGCGCCATCTGGGGCGCCTCCGCGTGGCTGTCATTCTAAGCGGCGCTGC‑G‑A‑TGGGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGt                                                                                   <  2:254034/144‑1 (MQ=255)
                                                             gCTCGACCGTGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGC‑GCC‑ACCCCCCCCCAAAAAAACCCCA‑GGCAGAGGGAAACGGAGTGGAGTTAGGTACCATGtag                                                                                 >  6:246141/1‑146 (MQ=255)
                                                                               cTTGCTGCCCGCGGCCGGCCGCGCCATCGGCGGCGCCGCCGCCTGGCTGTATTTCGAATCGGCGCGGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTgg                                                              <  4:425414/149‑1 (MQ=255)
                                                                                  gCTGCCCGCCGCCGGCAGCGCATTCTGCGGCGCCGCCGCGGTGCTGGAATTCGAAGCGGCGCGGC‑G‑C‑TGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGa                                                           <  2:2393/149‑1 (MQ=255)
                                                                                         gccgccgGGAGCGCCATGGGGGGGGCCGCCGCGGTGGTGCATTTCCATTCGGGGGGGC‑G‑C‑CGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGc                                                    <  2:60441/149‑1 (MQ=255)
                                                                                         gccgccgGCAGCGCCATCTGCGGCGCCGCCGCCGTGGTGGAATTCTAATCGGCGCTGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGc                                                    <  4:263611/149‑1 (MQ=255)
                                                                                           cccgggCAGCGCCTTCTGCGGCGCCGCCGCGTGGCTGGAATTCCAAGCGGCGCGGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCAGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCg                                                  <  6:78672/145‑1 (MQ=255)
                                                                                                  cgcgcCATCGGCGGCGCCGCCGCGGTGGTGGCATTCGATTCGGCGCTGC‑G‑C‑CGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggctggct                                           <  7:234841/148‑1 (MQ=255)
                                                                                                      ccATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGC‑G‑C‑AGCGCCCCCCAAAAAAACGCCAAGGCAGTCGGAAGCGTATTGCTGTTAGGTACCTTGTCGATTTTACATTACCCACAGGCGCTCAATGACggctggcgggc                                        >  8:125429/1‑144 (MQ=255)
                                                                                                        aTCGGCGGCGCCGCCGCGGTGGTGTCATTCCAAGCGGCGCGGC‑G‑C‑CGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCt                                     <  5:106345/149‑1 (MQ=255)
                                                                                                          cggcggcgCCGCCGGGGGTCGGTCATTCCACGCGGCGCGGC‑G‑C‑CCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCt                                     <  5:133426/145‑1 (MQ=255)
                                                                                                           tGCGGCGCCGCCGCGGTGCTGTAATTCGAATCGGCGCTGC‑G‑C‑TGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGa                                  <  8:320071/149‑1 (MQ=255)
                                                                                                               gcgcCGCCGCCGGGCTGGCATTCGAAGCGGCGCTGC‑G‑C‑TGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATAcc                              <  2:259696/149‑1 (MQ=255)
                                                                                                                            gCTGGCATTCGAATCGGCGCTGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTAGGTAACTTGTCGATGTTGCTTTAACACCTGGCGATAAATGACGGCTGGCTGCATCTGGATACCATTGGCGCCGGgc                 >  8:62557/1‑149 (MQ=255)
                                                                                                                               ggCATTCTATTGGGGGCGGC‑G‑C‑TGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGgctg               <  2:448058/148‑1 (MQ=255)
                                                                                                                                      gccgcGGGGCGGC‑G‑C‑CGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTggg       <  7:167732/145‑1 (MQ=255)
                                                                                                                                          cggcgcggc‑g‑C‑CGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGggcggc   <  4:84713/149‑1 (MQ=255)
                                                                                                                                           ggcgcggc‑g‑c‑CGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCa  <  6:40511/149‑1 (MQ=255)
                                                                                                                                           cgcgcGGC‑C‑C‑CGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCa  <  5:246141/148‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                                  
CGGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCA  >  NC_002947_CJ‑RC/4158322‑4158609

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