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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

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% 197.1 / NA 61pseudogene (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 (33/28);  total (33/28)

CGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTC  >  NC_000913/3815733‑3815998
                                                                                                                                    |                                                                                                                                       
cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATg                                                                                                                                  >  1:1184413/1‑139 (MQ=255)
cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATg                                                                                                                                  >  1:799888/1‑139 (MQ=255)
                 ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCgg                                                                                                                 >  1:589526/1‑139 (MQ=255)
                   cgcTGATATGGTTTCATGCCTTCGCTCCTCATC‑TACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGcc                                                                                                              >  2:1243408/1‑139 (MQ=255)
                      tGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCag                                                                                                            <  2:92650/139‑1 (MQ=255)
                        atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCagag                                                                                                          >  1:141130/1‑139 (MQ=255)
                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGa                                                                                                 >  1:1288209/1‑139 (MQ=255)
                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACaa                                                                                                                                    <  2:16584/103‑1 (MQ=255)
                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACaa                                                                                                                                    >  1:16584/1‑103 (MQ=255)
                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCggg                                                                                                                <  1:1087658/123‑1 (MQ=255)
                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCggg                                                                                                                >  2:1087658/1‑123 (MQ=255)
                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGAt                                                                                                >  2:202836/1‑139 (MQ=255)
                                  aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGAt                                                                                                >  1:458598/1‑139 (MQ=255)
                                   tGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                               <  1:202836/139‑1 (MQ=255)
                                   tGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                               <  2:799888/139‑1 (MQ=255)
                                   tGCCTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                               >  1:374476/1‑139 (MQ=255)
                                     ccTTCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                                                                             <  2:374476/139‑1 (MQ=255)
                                       ttCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                         >  2:1090686/1‑109 (MQ=255)
                                       ttCGCTCCTCATCTTACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                         <  1:1090686/109‑1 (MQ=255)
                                                     tACTTTTCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTg                                                                             >  1:143058/1‑139 (MQ=255)
                                                         tttCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                          >  1:620831/1‑122 (MQ=255)
                                                         tttCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                          <  2:620831/122‑1 (MQ=255)
                                                          ttCTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTAAAATGGATTGGATTCCCCt                                                                                                                    >  2:308811/1‑95 (MQ=255)
                                                          ttCTACAAACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                                                    <  1:308811/95‑1 (MQ=255)
                                                            cTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                                               >  2:294230/1‑98 (MQ=255)
                                                            cTACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                                               <  1:294230/98‑1 (MQ=255)
                                                             tACAGACA‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                                     >  2:711423/1‑139 (MQ=255)
                                                                  gacaaaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCt                                                                 >  1:78116/5‑139 (MQ=255)
                                                                   acaaaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                >  1:336355/4‑139 (MQ=255)
                                                                   acaaaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                >  1:1200197/4‑139 (MQ=255)
                                                                   acaaaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                >  2:116751/4‑139 (MQ=255)
                                                                       aaaaaaaaGCGACTCATCAGTCCCCTTTAAAATCATTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCCATTCCCCTCGGGCCAGTGCCAACAAGATGAGGAGGTCTTCAGGGGTGAACGGCTCGtcttcttc                                                            >  2:921597/1‑137 (MQ=255)
                                                                         aaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCg                                                          <  2:78116/139‑1 (MQ=255)
                                                                          aaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGcc                                                                                                        >  1:812793/1‑92 (MQ=255)
                                                                          aaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGcc                                                                                                        <  2:812793/92‑1 (MQ=255)
                                                                            aaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcc                                                       <  1:711423/139‑1 (MQ=255)
                                                                            aaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcc                                                       <  2:1184413/139‑1 (MQ=255)
                                                                             aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGc                                                            >  1:248902/1‑133 (MQ=255)
                                                                             aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGc                                                            <  2:248902/133‑1 (MQ=255)
                                                                               gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccctg                                                    <  2:458598/139‑3 (MQ=255)
                                                                               gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccctg                                                    <  2:336355/139‑3 (MQ=255)
                                                                               gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccctg                                                    <  2:141130/139‑3 (MQ=255)
                                                                                      atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCa                                            >  2:189245/1‑139 (MQ=255)
                                                                                             gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATgc                                     >  1:332505/1‑139 (MQ=255)
                                                                                                         aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                  <  1:967941/99‑1 (MQ=255)
                                                                                                         aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                  >  2:967941/1‑99 (MQ=255)
                                                                                                         aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCgg                         <  1:1243408/139‑1 (MQ=255)
                                                                                                          gTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCGGt                        <  2:717615/139‑1 (MQ=255)
                                                                                                          gTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCGGt                        >  1:1178297/1‑139 (MQ=255)
                                                                                                           tttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                          >  1:1242624/1‑73 (MQ=255)
                                                                                                           tttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                          <  2:1242624/73‑1 (MQ=255)
                                                                                                           tttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTc                           >  1:332961/1‑135 (MQ=255)
                                                                                                           tttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGAGGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTc                           <  2:332961/135‑1 (MQ=255)
                                                                                                            ttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                      <  2:1178297/139‑1 (MQ=255)
                                                                                                              gCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatc                    <  2:143058/139‑1 (MQ=255)
                                                                                                                cAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                  <  2:332505/139‑1 (MQ=255)
                                                                                                                     ccgccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCGGt                        <  2:578741/128‑1 (MQ=255)
                                                                                                                     ccgccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCGGt                        >  1:578741/1‑128 (MQ=255)
                                                                                                                        ccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGt                                                         <  2:491950/93‑1 (MQ=255)
                                                                                                                        ccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGt                                                         >  1:491950/1‑93 (MQ=255)
                                                                                                                                gTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGT‑CCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtc  >  2:874845/1‑139 (MQ=255)
                                                                                                                                    |                                                                                                                                       
CGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTC  >  NC_000913/3815733‑3815998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A