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
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,908 Δ1 bp pseudogene (642/669 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_0009133,815,9080T.100.0% 108.3 / NA 27pseudogene (642/669 nt)rphribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (14/13);  total (14/13)

AAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACG  >  NC_000913/3815803‑3816019
                                                                                                         |                                                                                                               
aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCg                                                                               >  2:881922/1‑139 (MQ=255)
      ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCt                                                                         >  2:833461/1‑139 (MQ=255)
                              aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                                                 <  1:808157/139‑1 (MQ=255)
                                    ttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                           <  1:881922/139‑1 (MQ=255)
                                     tGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCt                                                                                           >  1:729162/1‑90 (MQ=255)
                                     tGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCt                                                                                           <  2:729162/90‑1 (MQ=255)
                                                            ttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTg                                                                                                  <  2:386695/59‑1 (MQ=255)
                                                            ttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTg                                                                                                  >  1:386695/2‑60 (MQ=255)
                                                                 aTGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa              >  1:1168328/1‑139 (MQ=255)
                                                                      ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                        >  2:776054/1‑76 (MQ=255)
                                                                      ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                        <  1:776054/76‑1 (MQ=255)
                                                                      ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc         >  2:70199/1‑139 (MQ=255)
                                                                        cgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCtt       <  1:556021/139‑1 (MQ=255)
                                                                         gattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCtt                                                                                                          >  1:1305464/1‑39 (MQ=255)
                                                                         gattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCtt                                                                                                          <  2:1305464/39‑1 (MQ=255)
                                                                              cccTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                                  <  2:24391/90‑1 (MQ=255)
                                                                              cccTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                                  >  1:24391/1‑90 (MQ=255)
                                                                                        agagCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg                                              >  2:985506/1‑84 (MQ=255)
                                                                                        agagCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg                                              <  1:985506/84‑1 (MQ=255)
                                                                                               acaaGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                                                 <  2:1293457/74‑1 (MQ=255)
                                                                                               acaaGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                                                 >  1:1293457/1‑74 (MQ=255)
                                                                                               acaaGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACg                                   <  2:1368419/88‑1 (MQ=255)
                                                                                               acaaGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACg                                   >  1:1368419/1‑88 (MQ=255)
                                                                                               acaaGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACg  >  2:222368/1‑121 (MQ=255)
                                                                                               acaaGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACg  <  1:222368/121‑1 (MQ=255)
                                                                                                   gATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                          <  2:328894/77‑1 (MQ=255)
                                                                                                   gATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                          >  1:328894/1‑77 (MQ=255)
                                                                                                         |                                                                                                               
AAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACG  >  NC_000913/3815803‑3816019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A