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 F1 I1 R1 770 51.4 2439994 93.8% 2288714 110.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,883 Δ1 bp pseudogene (667/669 nt) rph ← ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,8800C.100.0% 195.4 / NA 47pseudogene (2/48 nt)rphribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (22/25);  total (22/25)

TGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCT  >  NC_000913/3815749‑3816013
                                                                                                                                    |                                                                                                                                     
tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCggg                                                                                                                               >  2:392453/1‑139 (MQ=255)
   cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGc                                                                                                                              >  2:421144/1‑137 (MQ=255)
   cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGc                                                                                                                              <  1:421144/137‑1 (MQ=255)
     cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCaga                                                                                                                          <  2:433735/139‑1 (MQ=255)
                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGcc                                                                                                                             >  2:27651/1‑123 (MQ=255)
                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGcc                                                                                                                             <  1:27651/123‑1 (MQ=255)
                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAg                                                                                                            >  1:577100/1‑139 (MQ=255)
                   tGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGAt                                                                                                               <  2:475995/136‑1 (MQ=255)
                   tGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGAt                                                                                                               >  1:475995/1‑136 (MQ=255)
                      cTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  1:392453/139‑1 (MQ=255)
                           ctcctcATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                                    <  2:229838/139‑1 (MQ=255)
                                   cTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCca                                                                                                                      <  2:737931/113‑1 (MQ=255)
                                   cTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCca                                                                                                                      >  1:737931/1‑113 (MQ=255)
                                      aCTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAc                                                                                         >  2:641651/1‑139 (MQ=255)
                                        ttttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         >  1:291271/1‑121 (MQ=255)
                                        ttttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  2:291271/121‑1 (MQ=255)
                                           tCTACAGACAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCt                                                                                     >  2:211670/1‑139 (MQ=255)
                                           tCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  2:587767/118‑1 (MQ=255)
                                           tCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         >  1:587767/1‑118 (MQ=255)
                                             tACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGc                                                                                  >  2:675772/1‑139 (MQ=255)
                                                  aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAg                                                                                                                 >  1:346459/1‑103 (MQ=255)
                                                  aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAg                                                                                                                 <  2:346459/103‑1 (MQ=255)
                                                  aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  <  1:1006462/118‑1 (MQ=255)
                                                  aC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  >  2:1006462/1‑118 (MQ=255)
                                                         aaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                       <  1:855412/139‑1 (MQ=255)
                                                          aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcc                                                                      >  1:508484/1‑139 (MQ=255)
                                                           aaGGCGACTCTTCAGTCGCCTTAAAAGTCAGATTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                     <  1:1212708/139‑1 (MQ=255)
                                                             ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGc                                                                                                                              <  2:140505/80‑1 (MQ=255)
                                                             ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGc                                                                                                                              >  1:140505/1‑80 (MQ=255)
                                                                 aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCag                                                                                                                           <  2:665104/79‑1 (MQ=255)
                                                                 aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCag                                                                                                                           >  1:665104/1‑79 (MQ=255)
                                                                    catcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCagag                                                                                                                         <  1:532553/78‑1 (MQ=255)
                                                                    catcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCagag                                                                                                                         >  2:532553/1‑78 (MQ=255)
                                                                        aGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatg                                                        >  1:530576/1‑139 (MQ=255)
                                                                             ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAg                                                                                                                 >  1:78558/1‑77 (MQ=255)
                                                                             ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAg                                                                                                                 <  2:78558/77‑1 (MQ=255)
                                                                                    aaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                            <  2:530576/139‑1 (MQ=255)
                                                                                        aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGt                                              <  1:111232/133‑1 (MQ=255)
                                                                                        aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGt                                              >  2:111232/1‑133 (MQ=255)
                                                                                          tttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtc                                      <  2:508484/139‑1 (MQ=255)
                                                                                            tGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                    <  2:615998/139‑1 (MQ=255)
                                                                                             gCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  >  1:832044/1‑76 (MQ=255)
                                                                                             gCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  <  2:832044/76‑1 (MQ=255)
                                                                                               cAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                 <  1:641651/139‑1 (MQ=255)
                                                                                               cAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                 <  2:967941/139‑1 (MQ=255)
                                                                                                    ccgccTTCTGCGTCGTTACAATGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                            <  2:497213/139‑1 (MQ=255)
                                                                                                                        aTGGATTCGATT‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa        >  2:449698/1‑139 (MQ=255)
                                                                                                                           gattcgatt‑cCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATCTCGGTCTCTGCGGCagag     <  1:675772/139‑1 (MQ=255)
                                                                                                                             ttcgatt‑cCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  >  2:783251/1‑44 (MQ=255)
                                                                                                                             ttcgatt‑cCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCCTCa                                                                                                  <  1:783251/44‑1 (MQ=255)
                                                                                                                              tcgatt‑cCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCt  >  2:678157/1‑139 (MQ=255)
                                                                                                                                    |                                                                                                                                     
TGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCT  >  NC_000913/3815749‑3816013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A