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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,712,518 (C)6→7 intergenic (+360/‑251) nth → / → dtpA DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,712,5121.C100.0% 188.7 / NA 55intergenic (+354/‑257)nth/dtpADNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (27/28);  total (27/28)

TCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAC  >  NC_000913/1712377‑1712637
                                                                                                                                        |                                                                                                                             
tCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccc                                                                                                                            <  1:205019/139‑1 (MQ=255)
  aGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          <  1:325345/139‑1 (MQ=255)
    gTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccccc                                                                                                                        >  1:1078850/1‑138 (MQ=255)
               ttAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgcag                                                                                                              >  1:818558/1‑139 (MQ=255)
                                         gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTACCGTAACGtttttt                                                                                    >  2:971839/1‑139 (MQ=255)
                                                 aaaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAAtt                                                                            <  2:637559/139‑1 (MQ=255)
                                                      ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  1:971839/139‑1 (MQ=255)
                                                      ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  1:1325948/139‑1 (MQ=255)
                                                       tACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGc                                                                      >  2:1437286/1‑139 (MQ=255)
                                                        acacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCt                                                                     >  1:323167/1‑139 (MQ=255)
                                                           cTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                                  <  1:1053249/139‑1 (MQ=255)
                                                              gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                               >  1:1207358/1‑139 (MQ=255)
                                                              gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                               >  2:564665/1‑139 (MQ=255)
                                                              gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                               >  1:1180696/1‑139 (MQ=255)
                                                              gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          <  2:1146036/79‑1 (MQ=255)
                                                              gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          >  1:1146036/1‑79 (MQ=255)
                                                              acTATTTTTCAGAAACTGGACTATCTAACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCACCACCCCCCCTCTCAGTGCAGTGAAAAAATCTACCGTCACGTGTTTTGAAAAATTTAACACTGGATaa                                                               >  1:30297/2‑139 (MQ=255)
                                                                   ttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       >  1:47369/1‑126 (MQ=255)
                                                                   ttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAAAAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  2:47369/126‑1 (MQ=255)
                                                                          aaaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                                   <  2:323167/139‑1 (MQ=255)
                                                                                gACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTg                                             >  1:804899/1‑139 (MQ=255)
                                                                                    aTCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAAtt                                         >  2:526095/1‑139 (MQ=255)
                                                                                     tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgc                                                                                                                >  2:1460196/1‑67 (MQ=255)
                                                                                     tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgc                                                                                                                <  1:1460196/67‑1 (MQ=255)
                                                                                     tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTc                                        <  1:1471357/139‑1 (MQ=255)
                                                                                       tcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                                      <  1:1273244/139‑1 (MQ=255)
                                                                                          cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccccctct                                                                                                                     <  2:1249004/56‑5 (MQ=255)
                                                                                          cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccccctct                                                                                                                     >  1:1249004/1‑52 (MQ=255)
                                                                                           tAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  <  2:153308/139‑1 (MQ=255)
                                                                                            aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  2:1207358/139‑1 (MQ=255)
                                                                                             gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATc                                                                                                    >  1:1126184/1‑71 (MQ=255)
                                                                                             gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATc                                                                                                    <  2:1126184/71‑1 (MQ=255)
                                                                                               aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATATGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCGAGAATGGTTGAATTCCCCGCCTCAg                              >  1:1399269/1‑139 (MQ=255)
                                                                                                aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          >  1:805538/1‑45 (MQ=255)
                                                                                                aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          <  2:805538/45‑1 (MQ=255)
                                                                                                 aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGtt                            <  1:526095/139‑1 (MQ=255)
                                                                                                 aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          <  1:795516/44‑1 (MQ=255)
                                                                                                 aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          >  2:795516/1‑44 (MQ=255)
                                                                                                     gCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAGATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 >  1:818290/1‑130 (MQ=255)
                                                                                                     gCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  2:818290/130‑1 (MQ=255)
                                                                                                         aaTAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                    <  2:818558/139‑1 (MQ=255)
                                                                                                               aGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgca                                                                                                               <  2:1096352/42‑1 (MQ=255)
                                                                                                               aGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgca                                                                                                               >  1:1096352/1‑42 (MQ=255)
                                                                                                               aGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                   >  1:833592/1‑118 (MQ=255)
                                                                                                               aGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                   <  2:833592/118‑1 (MQ=255)
                                                                                                                 aaCATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGa                >  1:259743/1‑135 (MQ=255)
                                                                                                                 aaCATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGa                <  2:259743/135‑1 (MQ=255)
                                                                                                                   cATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                    <  1:310509/129‑1 (MQ=255)
                                                                                                                   cATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                    >  2:310509/1‑129 (MQ=255)
                                                                                                                   cATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGAttatta          >  1:757055/1‑139 (MQ=255)
                                                                                                                     tatCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACa        <  1:564665/139‑1 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa                                                                         <  2:747234/71‑1 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa                                                                         >  1:747234/1‑71 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       >  2:738763/1‑73 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  1:738763/73‑1 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTcc                                                        <  1:1296405/88‑1 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTcc                                                        >  2:1296405/1‑88 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  2:16599/111‑1 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  1:663665/111‑1 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 >  2:663665/1‑111 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 >  1:16599/1‑111 (MQ=255)
                                                                                                                           cGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGCAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAc  <  2:757055/139‑1 (MQ=255)
                                                                                                                              tAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  <  2:1323239/104‑1 (MQ=255)
                                                                                                                              tAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  >  1:1323239/1‑104 (MQ=255)
                                                                                                                               aaGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  <  2:749633/103‑1 (MQ=255)
                                                                                                                               aaGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  >  1:749633/1‑103 (MQ=255)
                                                                                                                                        |                                                                                                                             
TCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAC  >  NC_000913/1712377‑1712637

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