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
A5 F216 I0 R1 247 44.8 1629152 98.0% 1596568 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,333,310 T→C 8.0% pseudogene (1093/4605 nt) yfaS ← pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,333,3100TC 8.0% 146.2 / 4.1 50pseudogene (1093/4605 nt)yfaSpseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein
Reads supporting (aligned to +/- strand):  ref base T (21/25);  new base C (2/2);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.56e-01

GAAACTTCCCTGCCCGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATCCTTACCCAGAATGTATGAAC  >  NC_000913/2333167‑2333456
                                                                                                                                               |                                                                                                                                                  
gAAACTTCCCTGCCCGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACt                                                                                                                                                <  4:66733/148‑1 (MQ=255)
  aaCTTCCCTGCCCGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTa                                                                                                                                             >  2:81279/1‑149 (MQ=255)
       cccTGCCCGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACAt                                                                                                                                         <  4:369050/148‑1 (MQ=255)
        ccTGCCCGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACa                                                                                                                                          <  2:262610/146‑1 (MQ=255)
        ccTGCCCGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCAGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACa                                                                                                                                          >  1:262610/1‑146 (MQ=255)
           gCCCGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCCGTTGGCGTCCTGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGaca                                                                                                                                    <  2:187561/149‑1 (MQ=255)
              cGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGa                                                                                                                                 >  1:317257/1‑149 (MQ=255)
                                         tGACGGTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATc                                                                                                       >  4:323978/1‑148 (MQ=255)
                                           tcGGTTTGCAACAGACTGACGTTGGCGTCCAGCATCGAAAGCTTCGCCGGGGCGCTGACGATGGTGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTTCGCGATATAGCGGGCGATCgg                                                                                                     <  4:34680/147‑1 (MQ=255)
                                              gTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTaaa                                                                                                 >  2:141918/1‑149 (MQ=255)
                                                    aaCAGACTGCCGTTGGCGTCCAGCACCGAGAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAatatt                                                                                           <  1:104340/149‑2 (MQ=255)
                                                     aCAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAAtata                                                                                           >  4:260416/1‑148 (MQ=255)
                                                             ccGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACCAGCGGgt                                                                                  <  2:221438/149‑1 (MQ=255)
                                                              cGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGgt                                                                                  >  3:364331/1‑148 (MQ=255)
                                                               gTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGACCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGgtg                                                                                 >  4:24545/1‑148 (MQ=255)
                                                                ttGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGtgtt                                                                               <  2:317257/149‑1 (MQ=255)
                                                                 tGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCggg                                                                                   <  4:118020/144‑1 (MQ=255)
                                                                 tGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCggg                                                                                   >  3:118020/1‑144 (MQ=255)
                                                                   gCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTa                                                                            <  2:177805/149‑1 (MQ=255)
                                                                     gTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGa                                                                          >  1:322744/1‑149 (MQ=255)
                                                                      tCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGa                                                                          >  3:404129/1‑148 (MQ=255)
                                                                      tCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGAt                                                                         <  2:322744/149‑1 (MQ=255)
                                                                          gCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGGGTTGTAGATTTc                                                                      >  4:6495/1‑148 (MQ=255)
                                                                              cGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATc                                                                                                                               >  2:299389/1‑87 (MQ=255)
                                                                              cGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATc                                                                                                                               <  1:299389/87‑1 (MQ=255)
                                                                              cGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCttt                                                                 <  2:143606/149‑1 (MQ=255)
                                                                               gAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTc                                                                <  2:65866/149‑1 (MQ=255)
                                                                                aaaGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCg                                                               >  2:14193/1‑149 (MQ=255)
                                                                                     ttCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGACCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTagaa                                                          >  2:268484/1‑149 (MQ=255)
                                                                                         ccGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGaagaag                                                      <  1:14193/149‑1 (MQ=255)
                                                                                                 cTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCgg                                               <  4:255081/148‑1 (MQ=255)
                                                                                                  tGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCg                                                <  2:75845/146‑1 (MQ=255)
                                                                                                  tGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCg                                                >  1:75845/1‑146 (MQ=255)
                                                                                                  tGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGgag                                             >  2:177231/1‑149 (MQ=255)
                                                                                                          ggggATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTc                                                                      <  2:58836/116‑1 (MQ=255)
                                                                                                          ggggATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTc                                                                      >  1:58836/1‑116 (MQ=255)
                                                                                                          ggggATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTc                                                                      >  1:246769/1‑116 (MQ=255)
                                                                                                          ggggATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTc                                                                      <  2:246769/116‑1 (MQ=255)
                                                                                                             gATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAAcgcc                                  <  1:141918/149‑1 (MQ=255)
                                                                                                                  aTGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCtt                             >  2:350832/1‑149 (MQ=255)
                                                                                                                       aCGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCa                        >  1:206356/1‑149 (MQ=255)
                                                                                                                         ggATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCAt                       <  4:364331/148‑1 (MQ=255)
                                                                                                                         ggATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATc                      <  1:81279/149‑1 (MQ=255)
                                                                                                                         ggATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATc                      <  1:196820/149‑1 (MQ=255)
                                                                                                                          gATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATcc                     <  1:356003/149‑1 (MQ=255)
                                                                                                                               tGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATCCTTAcc                <  1:177231/149‑1 (MQ=255)
                                                                                                                                     tCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATCCTTACCCAGaa           >  4:159237/1‑148 (MQ=255)
                                                                                                                                        cgGCCGACCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATCCTTACCCAGAATGTa       <  1:268484/149‑1 (MQ=255)
                                                                                                                                         ggCCGACCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATCCTTACCCAGAATGTa       <  3:24545/148‑1 (MQ=255)
                                                                                                                                             gATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATCCTTACCCAGAATGTATGAAc  >  1:143593/1‑149 (MQ=255)
                                                                                                                                               |                                                                                                                                                  
GAAACTTCCCTGCCCGCCATTGCGCGCATCCAGCGTGACATTGACGGTTTGCAACAGACTGCCGTTGGCGTCCAGCACCGAAAGCTTCGCCGGGGCGCTGACGATGGGGGATGAATGCAACGGATCGTGGAACTCGCGGCCGATCACTTTAACATCGACACGATCGCCTGCGCGATATAGCGGGCGATCGGTAAAAATATACAAGCGGGTGTTGTAGATTTCGCTTTCGTAGAAGAAGTTCTCGGAGACAAAAACGCCGCCTTCAGCATCCTTACCCAGAATGTATGAAC  >  NC_000913/2333167‑2333456

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A