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
A17 F3 I1 R1 15 66.3 2212468 93.9% 2077507 141.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 2,679,525 G→T A1074D (GCT→GAT)  yphG ← DUF4380 domain‑containing TPR repeat protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA2,679,5250GT100.0% 163.1 / NA 49A1074D (GCT→GAT) yphGDUF4380 domain‑containing TPR repeat protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (19/30);  total (19/30)

GGTTTTTATTAACAACGGCTTAT‑TCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGGT  >  NC_000913_3_pae_tpiA/2679382‑2679668
                                                                                                                                                 |                                                                                                                                               
gggttttATGAACAACGGCTTAT‑TTGAATTATTTTGTGATGAGCGGGAGCGCGTGCCGCTAAAATATTACAGTTAATAGGGTTG‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGa                                                                                                                                            <  2:112446/146‑1 (MQ=255)
ggTTTTTATTAACAACGGCTTATCTCT‑TTTATTTTGTGCTGCGGACAATCTCGTTCCGCTCAAATATTACAGTTAAGAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGa                                                                                                                                            <  1:252559/149‑1 (MQ=255)
             aacGGCTTAT‑TCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCa                                                                                                                               >  1:995485/1‑149 (MQ=255)
                ggCTTAT‑TGTATGTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAAtt                                                                                                                            <  2:902949/149‑1 (MQ=255)
                ggCTTAT‑TCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAAtt                                                                                                                            <  1:347935/149‑1 (MQ=255)
                 gCTTAT‑TCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTc                                                                                                                           >  1:244668/1‑149 (MQ=255)
                            attattTTGTGATGAGCGGCAGCTCGTGCCGCTCAAATATTACATTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCa                                                                                                                 <  1:551800/149‑1 (MQ=255)
                                ttttGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACt                                                                                                             >  1:207892/1‑149 (MQ=255)
                                        tgaGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTgc                                                                                                     <  1:904852/149‑1 (MQ=255)
                                         gaGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGTCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTgcg                                                                                                    <  1:929005/149‑1 (MQ=255)
                                                 gggcgTGCCGGTCAAATATTATAGTTAATGGGGTTTAAGTG‑ACTCGGTTAAAAAAAAAAGGCATCGCGGTTGTGAATAATGCCGCTTTCGGCCAATCCGGATTAACCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTcc                                                                                            <  2:179854/147‑1 (MQ=255)
                                                  cgcgTGCCGGTCAAATATTACTGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCGACCTccc                                                                                           <  2:752523/149‑1 (MQ=255)
                                                   gcgTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTcccc                                                                                          <  1:86595/149‑1 (MQ=255)
                                                     gTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGa                                                                                        <  1:737535/149‑1 (MQ=255)
                                                      tGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAg                                                                                       <  1:564053/149‑1 (MQ=255)
                                                        ccGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTc                                                                                     <  1:244750/149‑1 (MQ=255)
                                                          gCTTAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc                                                                                   <  2:885863/149‑1 (MQ=255)
                                                                atatTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAc                                                                             >  1:502520/1‑149 (MQ=255)
                                                                 tatTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACg                                                                            >  2:714317/1‑149 (MQ=255)
                                                                  atTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCACCCTCCCCGAGTCCCGCGGACGc                                                                           >  1:301789/1‑149 (MQ=255)
                                                                  atTACAGTTAATAGGCTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTATCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTACGCAACCTCCCCGAGTCCCGCGGACGc                                                                           >  2:907888/1‑149 (MQ=255)
                                                                    tACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCa                                                                         <  2:502520/149‑1 (MQ=255)
                                                                     aCAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGa                                                                                                                    >  1:948203/1‑105 (MQ=255)
                                                                     aCAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGa                                                                                                                    <  2:948203/105‑1 (MQ=255)
                                                                       aGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCa                                                                      >  2:182824/1‑149 (MQ=255)
                                                                                        tGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCACCAGGCa                                                      >  1:663678/1‑149 (MQ=255)
                                                                                          aaCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAg                                                                                                                   >  2:315720/1‑86 (MQ=255)
                                                                                          aaCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAg                                                                                                                   <  1:315720/86‑1 (MQ=255)
                                                                                             gcgGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAc                                                                             <  1:616483/121‑1 (MQ=255)
                                                                                             gcgGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAc                                                                             >  2:616483/1‑121 (MQ=255)
                                                                                               ggTTAACAATAAAAGGCATCACGGCAGTGAATCCTGCCTCTTTCGTCCAATCCGGATTAATCGCCGTCAATTAAGCGCGAGCTGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCACCAGGCATTTTTCt                                               <  1:581615/149‑1 (MQ=255)
                                                                                                 ttAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAAtt                                                                                                                            >  1:862593/1‑70 (MQ=255)
                                                                                                 ttAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAAtt                                                                                                                            <  2:862593/70‑1 (MQ=255)
                                                                                                    aaaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGGGCAGACTCATCTTCCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGCCATGTTTCTTTAtc                                          >  1:441735/1‑148 (MQ=255)
                                                                                                    aaaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAtg                                          <  1:341444/149‑1 (MQ=255)
                                                                                                       aTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAtgctg                                       >  1:838709/1‑149 (MQ=255)
                                                                                                        tAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAtgctgt                                      <  1:47539/149‑2 (MQ=255)
                                                                                                        tAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAtgctgc                                      >  1:975518/1‑149 (MQ=255)
                                                                                                         aaaaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATgctgct                                     <  1:714317/149‑1 (MQ=255)
                                                                                                          aaaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGctgctg                                    <  2:1027273/149‑1 (MQ=255)
                                                                                                            aGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgtt                                  <  1:610694/149‑1 (MQ=255)
                                                                                                              gCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgttgt                                <  1:817869/149‑1 (MQ=255)
                                                                                                                  cACGGCGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAAt                            <  1:561948/149‑1 (MQ=255)
                                                                                                                          tgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATAc                    <  1:624944/149‑1 (MQ=255)
                                                                                                                            aataatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAc                                                                             <  2:22574/90‑1 (MQ=255)
                                                                                                                            aataatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAc                                                                             >  1:22574/1‑90 (MQ=255)
                                                                                                                                  gctccTTTGGGCCACTCCGGATTAATCGCCGTCAATTGCGGGCGAGCAGACTCATATTGCGCAACCTCCTCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATAAGGAGacaa            <  2:136978/145‑1 (MQ=255)
                                                                                                                                           ggCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAgg   >  1:107574/1‑149 (MQ=255)
                                                                                                                                            gCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGGCAGGt  >  1:189003/1‑149 (MQ=255)
                                                                                                                                                 |                                                                                                                                               
GGTTTTTATTAACAACGGCTTAT‑TCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTT‑AGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGGT  >  NC_000913_3_pae_tpiA/2679382‑2679668

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A