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
A4 F28 I1 R1 128 54.7 1845674 99.3% 1832754 139.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,808,753 C→T pseudogene (438/1178 nt) ygaY → putative transporter YgaY, N‑terminal fragment

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,808,7530CT100.0% 136.1 / NA 39pseudogene (438/1178 nt)ygaYputative transporter YgaY, N‑terminal fragment
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/17);  total (22/17)

TCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAATCAGAAACCCAC  >  NC_000913/2808619‑2808887
                                                                                                                                      |                                                                                                                                      
tCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCa                                                                                                                                   >  2:410099/1‑140 (MQ=255)
tCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCa                                                                                                                                   >  1:75979/1‑140 (MQ=255)
  ggTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACg                                                                                                                                 >  2:809890/1‑140 (MQ=255)
    tACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGa                                                                                                                               <  2:75979/140‑1 (MQ=255)
    tACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGCTCTGCTGTTGGGGATCTTGTTGGCACGGa                                                                                                                               <  2:662438/140‑1 (MQ=255)
       ggCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAg                                                                                                                            >  2:264164/1‑140 (MQ=255)
           ttAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGc                                                                                                                        <  1:41188/140‑1 (MQ=255)
              aCCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCgg                                                                                                                     >  2:655059/1‑140 (MQ=255)
                   tttATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGc                                                                                                                >  2:894666/1‑140 (MQ=255)
                       ttCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGc                                                                                                            <  2:326611/140‑1 (MQ=255)
                            aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAAtc                                                                                                       >  1:500121/1‑140 (MQ=255)
                                 tGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTcggc                                                                                                  <  2:560207/140‑1 (MQ=255)
                                            cTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                                       <  1:533932/140‑1 (MQ=255)
                                            cTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                                       <  1:655059/140‑1 (MQ=255)
                                            cTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                                       <  2:422853/140‑1 (MQ=255)
                                                     cTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTg                                                                              >  2:553885/1‑140 (MQ=255)
                                                      tGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTgg                                                                             <  2:81335/140‑1 (MQ=255)
                                                        gCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGt                                                                           <  1:264164/140‑1 (MQ=255)
                                                          aGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTg                                                                         >  1:845746/1‑140 (MQ=255)
                                                            cGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCt                                                                       <  1:34151/140‑1 (MQ=255)
                                                                       tCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTCTTGGGTTGCTTCGGTGTTAAt                                                            <  2:653523/140‑1 (MQ=255)
                                                                              aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTg                                                     >  1:734677/1‑140 (MQ=255)
                                                                                     cgGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGgcgc                                              <  1:410099/140‑1 (MQ=255)
                                                                                     cgGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGgcgc                                              <  2:720911/140‑1 (MQ=255)
                                                                                        cAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTgg                                           <  1:551989/140‑1 (MQ=255)
                                                                                                    cACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTgg                                           <  2:910755/128‑1 (MQ=255)
                                                                                                    cACTATTATGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTgg                                           >  1:910755/1‑128 (MQ=255)
                                                                                                         ttatGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTg                          >  1:589542/1‑140 (MQ=255)
                                                                                                         ttatGAGCGGTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTg                          >  1:661311/1‑140 (MQ=255)
                                                                                                                 ggTCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAAt                  >  1:343704/1‑140 (MQ=255)
                                                                                                                   tCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGa                >  1:372571/1‑140 (MQ=255)
                                                                                                                   tCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGa                >  2:828975/1‑140 (MQ=255)
                                                                                                                   tCTGCTGTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGa                >  1:912220/1‑140 (MQ=255)
                                                                                                                    ctgctgTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGaa               <  1:876105/140‑1 (MQ=255)
                                                                                                                     tgctgTTGGGGATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGaaa              >  2:29427/1‑140 (MQ=255)
                                                                                                                             gggATCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAATCAGAAAc      >  2:899987/1‑140 (MQ=255)
                                                                                                                                 tCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAATCAGAAACCCAc  >  2:518615/1‑140 (MQ=255)
                                                                                                                                 tCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAATCAGAAACCCAc  >  1:550711/1‑140 (MQ=255)
                                                                                                                                 tCTTGTTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAATCAGAAACCCAc  >  2:414686/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                                      
TCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAATCAGAAACCCAC  >  NC_000913/2808619‑2808887

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