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
A3 F1 I2 R1 777 59.2 2955938 92.5% 2734242 106.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,863 C→T pseudogene (19/48 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_0009133,815,8630CT100.0% 165.9 / NA 52pseudogene (19/48 nt)rphribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/26);  total (26/26)

CTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCA  >  NC_000913/3815728‑3815981
                                                                                                                                       |                                                                                                                      
ctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACa                                                                                                                    <  2:480623/139‑1 (MQ=255)
               aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTATTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTccc                                                                                                     <  2:459071/139‑1 (MQ=255)
                 aaaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                                   <  2:1159869/139‑1 (MQ=255)
                                  gTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCcaacaa                                                                                  >  1:34960/1‑139 (MQ=255)
                                       aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAg                                                                                 >  2:1141732/1‑135 (MQ=255)
                                       aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAg                                                                                 <  1:1141732/135‑1 (MQ=255)
                                       aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGa                                                                             >  1:804051/1‑139 (MQ=255)
                                        tGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                            <  2:1274671/139‑1 (MQ=255)
                                        tGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                            >  1:334682/1‑139 (MQ=255)
                                           cTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                         <  1:306151/139‑1 (MQ=255)
                                             tCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                            >  1:275997/1‑134 (MQ=255)
                                             tCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                            <  2:275997/134‑1 (MQ=255)
                                                                tCTACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                    >  1:1039414/1‑139 (MQ=255)
                                                                  tACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcga                                                                                                          >  1:1092350/1‑83 (MQ=255)
                                                                  tACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcga                                                                                                          <  2:1092350/83‑1 (MQ=255)
                                                                  tACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                            >  2:843661/1‑113 (MQ=255)
                                                                  tACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                            <  1:843661/113‑1 (MQ=255)
                                                                  tACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACgg                                                       >  1:1440739/1‑134 (MQ=255)
                                                                  tACAGAC‑AAAAAAAGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACgg                                                       <  2:1440739/134‑1 (MQ=255)
                                                                          aaaaaaaGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                    >  2:721896/1‑114 (MQ=255)
                                                                          aaaaaaaGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                    <  1:721896/114‑1 (MQ=255)
                                                                             aaaaGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGt                                        >  2:850509/1‑139 (MQ=255)
                                                                               aaGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                                   >  1:979285/1‑78 (MQ=255)
                                                                               aaGGTGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                                   <  2:979285/78‑1 (MQ=255)
                                                                                  gtgACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACa                                                                                                                    >  1:575772/3‑58 (MQ=255)
                                                                                  gtgACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACa                                                                                                                    <  2:575772/56‑1 (MQ=255)
                                                                                  gtgACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                                   >  1:1363983/3‑75 (MQ=255)
                                                                                  gtgACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                                   <  2:1363983/73‑1 (MQ=255)
                                                                                   tgACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                  <  2:34960/138‑1 (MQ=255)
                                                                                    gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCAt                                                                 >  2:218832/1‑107 (MQ=255)
                                                                                    gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCAt                                                                 <  1:218832/107‑1 (MQ=255)
                                                                                           caGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCaa                          <  2:334682/139‑1 (MQ=255)
                                                                                               cGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCa                                                                                            <  2:1060577/69‑1 (MQ=255)
                                                                                               cGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCa                                                                                            >  1:1060577/1‑69 (MQ=255)
                                                                                                 ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                  <  1:1265268/125‑1 (MQ=255)
                                                                                                 ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                  >  2:1265268/1‑125 (MQ=255)
                                                                                                 ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgc                    >  1:1269659/1‑139 (MQ=255)
                                                                                                   ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGct                                                                       >  2:492400/1‑86 (MQ=255)
                                                                                                   ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGct                                                                       <  1:492400/86‑1 (MQ=255)
                                                                                                   ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                  <  1:251418/123‑1 (MQ=255)
                                                                                                   ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                  >  2:251418/1‑123 (MQ=255)
                                                                                                   ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                  >  1:641004/1‑139 (MQ=255)
                                                                                                         aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt            <  2:641004/139‑1 (MQ=255)
                                                                                                              tttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGGACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt       >  2:972720/1‑139 (MQ=255)
                                                                                                                tGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca     <  1:850509/139‑1 (MQ=255)
                                                                                                                   cAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca  >  1:998904/1‑139 (MQ=255)
                                                                                                                        ccgccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                    <  1:1324586/100‑1 (MQ=255)
                                                                                                                        ccgccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                    >  2:1324586/1‑100 (MQ=255)
                                                                                                                           ccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca     >  2:1202172/1‑128 (MQ=255)
                                                                                                                           ccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca     <  1:1202172/128‑1 (MQ=255)
                                                                                                                                 gCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg         <  2:1121916/118‑1 (MQ=255)
                                                                                                                                 gCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg         >  1:1121916/1‑118 (MQ=255)
                                                                                                                                       |                                                                                                                      
CTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCA  >  NC_000913/3815728‑3815981

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A