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
A10 F1 I1 R1 759 65.2 3386260 90.7% 3071337 101.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,994,415 G→A pseudogene (34/60 nt) pbl → pseudogene, peptidoglycan‑binding enzyme family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,994,4150GA100.0% 224.1 / NA 69pseudogene (34/60 nt)pblpseudogene, peptidoglycan‑binding enzyme family
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (34/35);  total (34/35)

GTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGT  >  NC_000913/2994297‑2994544
                                                                                                                      |                                                                                                                                 
gtgGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCa                                                                                                               >  1:1537089/1‑139 (MQ=255)
      tAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGa                                                                                                         >  2:229418/1‑139 (MQ=255)
         cGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGcc                                                                                                      >  1:344024/1‑139 (MQ=255)
         cGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGcc                                                                                                      >  1:1676205/1‑139 (MQ=255)
           tGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTa                                                                                                    >  2:703100/1‑139 (MQ=255)
             gCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTaaa                                                                                                  <  2:297863/139‑1 (MQ=255)
              cAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGc                                                                                                                      >  1:927404/1‑118 (MQ=255)
              cAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGc                                                                                                                      <  2:927404/118‑1 (MQ=255)
              cAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAg                                                                                                 >  2:1458701/1‑139 (MQ=255)
                   ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  1:703100/139‑1 (MQ=255)
                   ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  1:229418/139‑1 (MQ=255)
                   ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  2:1676205/139‑1 (MQ=255)
                     tGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCtt                                                                                                                    >  2:395703/1‑113 (MQ=255)
                     tGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCtt                                                                                                                    <  1:395703/113‑1 (MQ=255)
                             tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAg                                                                                                                 >  2:1296592/1‑108 (MQ=255)
                             tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAg                                                                                                                 <  1:1296592/108‑1 (MQ=255)
                             tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            >  1:223920/1‑129 (MQ=255)
                             tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  2:223920/129‑1 (MQ=255)
                             tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                  <  1:1458701/139‑1 (MQ=255)
                                   gCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGc                                                                            <  2:344024/139‑1 (MQ=255)
                                      ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            >  1:1509903/1‑120 (MQ=255)
                                      ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  2:1509903/120‑1 (MQ=255)
                                      ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                         <  2:1537089/139‑1 (MQ=255)
                                      ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                         >  1:1384087/1‑139 (MQ=255)
                                      ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                         >  2:1073352/1‑139 (MQ=255)
                                             cAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGCATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCAt                                                                  <  1:1073352/139‑1 (MQ=255)
                                                     aaCCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAg                                                          <  2:510021/139‑1 (MQ=255)
                                                       ccAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            >  1:147111/1‑103 (MQ=255)
                                                       ccAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  2:147111/103‑1 (MQ=255)
                                                       ccAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCt                                                        >  1:463915/1‑139 (MQ=255)
                                                           aaaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                         >  2:736992/1‑118 (MQ=255)
                                                           aaaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                         <  1:736992/118‑1 (MQ=255)
                                                                       cAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGa                                        <  2:463915/139‑1 (MQ=255)
                                                                                 cAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGa                                        <  1:892353/129‑1 (MQ=255)
                                                                                 cAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGa                                        >  2:892353/1‑129 (MQ=255)
                                                                                  aaaaTATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGa                             >  1:46542/1‑139 (MQ=255)
                                                                                           atTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAt                    <  2:46542/139‑1 (MQ=255)
                                                                                                atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                >  2:478297/1‑106 (MQ=255)
                                                                                                atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                <  1:478297/106‑1 (MQ=255)
                                                                                                atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCa                                   <  1:1494319/119‑1 (MQ=255)
                                                                                                atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCa                                   >  2:1494319/1‑119 (MQ=255)
                                                                                                atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttctt               >  1:248222/1‑139 (MQ=255)
                                                                                                  ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  2:1183706/60‑1 (MQ=255)
                                                                                                  ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            >  1:1183706/1‑60 (MQ=255)
                                                                                                   taCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCAt            <  2:1384087/139‑1 (MQ=255)
                                                                                                       aGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGata        <  2:248222/139‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            >  1:1174220/1‑53 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  2:1390579/53‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            >  2:1321592/1‑53 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  1:1321592/53‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  2:1174220/53‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            >  1:1390579/1‑53 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAg                                                          <  1:412623/87‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAg                                                          >  2:412623/1‑87 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                >  2:97331/1‑97 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                >  2:80304/1‑97 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                <  1:80304/97‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                <  1:97331/97‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                      >  1:648701/1‑107 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                      <  2:648701/107‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                      <  2:1183725/107‑1 (MQ=255)
                                                                                                         gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                      >  1:1183725/1‑107 (MQ=255)
                                                                                                             aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            >  1:877484/1‑49 (MQ=255)
                                                                                                             aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                            <  2:877484/49‑1 (MQ=255)
                                                                                                             aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGt  >  1:167330/1‑139 (MQ=255)
                                                                                                              aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtat                                                                                   >  2:1205289/1‑57 (MQ=255)
                                                                                                              aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtat                                                                                   <  1:1205289/57‑1 (MQ=255)
                                                                                                              aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGa                                        <  1:1362619/100‑1 (MQ=255)
                                                                                                              aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGa                                        >  2:1362619/1‑100 (MQ=255)
                                                                                                                      |                                                                                                                                 
GTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGT  >  NC_000913/2994297‑2994544

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