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 4,158,471 A→C 46.6% S161R (AGC→CGC)  PP_3661 → membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC4,158,4710AC46.6% ‑5.0 / 17.8 35S161R (AGC→CGC) PP_3661membrane protein
Reads supporting (aligned to +/- strand):  ref base A (8/6);  new base C (7/9);  total (15/20)
Fisher's exact test for biased strand distribution p-value = 7.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.37e-01

GGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTGTCCACG  >  NC_002947_CJ‑RC/4158323‑4158618
                                                                                                                                                       |                                                                                                                                                   
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)
                                                                                                                                                       aGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTGTCCACg  >  6:400854/1‑148 (MQ=255)
                                                                                                                                                       |                                                                                                                                                   
GGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGC‑G‑C‑AGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTGTCCACG  >  NC_002947_CJ‑RC/4158323‑4158618

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A