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
A8 F1 I2 R1 765 53.2 2691310 93.4% 2513683 103.8

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.C96.3% 185.9 / ‑0.2 54intergenic (+354/‑257)nth/dtpADNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (26/26);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑CC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAC  >  NC_000913/1712379‑1712637
                                                                                                                                       |                                                                                                                              
aGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc‑ccc                                                                                                                          <  2:122026/139‑1 (MQ=255)
aGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc‑ccc                                                                                                                          <  1:37506/139‑1 (MQ=255)
  gTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc‑ccccc                                                                                                                        >  2:336788/1‑138 (MQ=255)
                                       gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc‑ccccctct                                                                                                                     >  2:684457/1‑101 (MQ=255)
                                       gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc‑ccccctct                                                                                                                     <  1:684457/105‑5 (MQ=255)
                                         ccTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGa                                                                                  >  2:697825/1‑139 (MQ=255)
                                          cTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc                                                                                                                              >  2:837393/1‑94 (MQ=255)
                                          cTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc                                                                                                                              <  1:837393/94‑1 (MQ=255)
                                             cAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaaa                                                                              >  1:866199/1‑139 (MQ=255)
                                             cAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaaa                                                                              >  1:340197/1‑139 (MQ=255)
                                                    ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  2:154120/139‑1 (MQ=255)
                                                          tGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGAt                                                                 >  1:1080203/1‑139 (MQ=255)
                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTcagtgc                                                                                                                <  1:965647/90‑1 (MQ=255)
                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       >  1:1231594/1‑131 (MQ=255)
                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  2:1231594/131‑1 (MQ=255)
                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑CCGCCCCTCTcagtgc                                                                                                                >  2:965647/1‑90 (MQ=255)
                                                             cTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAAc                                                              >  2:1321077/1‑139 (MQ=255)
                                                                 ttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACAttt                                                          >  1:453966/1‑139 (MQ=255)
                                                                          aCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATg                                                 >  1:1034862/1‑139 (MQ=255)
                                                                              gACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTg                                             >  2:508622/1‑139 (MQ=255)
                                                                                        cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                                                     >  1:645632/1‑121 (MQ=255)
                                                                                        cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                                                     <  2:645632/121‑1 (MQ=255)
                                                                                        cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                   >  2:327169/1‑139 (MQ=255)
                                                                                          aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  1:467702/139‑1 (MQ=255)
                                                                                          aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  1:336788/139‑1 (MQ=255)
                                                                                          aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 >  2:467702/1‑139 (MQ=255)
                                                                                          aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  1:508622/139‑1 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAAc                                                                        >  1:1164450/1‑97 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAAc                                                                        <  2:1164450/97‑1 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAAc                                                              >  1:630203/1‑107 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAAc                                                              <  2:630203/107‑1 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                              <  2:1080203/139‑1 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                              >  2:1279549/1‑139 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                              <  2:475625/139‑1 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc‑ccc                                                                                                                          >  2:1210246/1‑46 (MQ=255)
                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑cc‑ccc                                                                                                                          <  1:1210246/46‑1 (MQ=255)
                                                                                             aaaaaCGCTAAATAACAGAACATATCGCCGTTAAGCCCTTCC‑CC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                              <  1:1240553/139‑1 (MQ=255)
                                                                                              aaaaCGCTAAATAGCAGAAGATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGt                             >  2:622394/1‑139 (MQ=255)
                                                                                              aaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCg                                    >  1:173343/1‑132 (MQ=255)
                                                                                              aaaaCGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCg                                    <  2:173343/132‑1 (MQ=255)
                                                                                                      aaaTAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                                                     >  1:306726/1‑107 (MQ=255)
                                                                                                      aaaTAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                                                     <  2:306726/107‑1 (MQ=255)
                                                                                                       aaTAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                    <  2:1034862/139‑1 (MQ=255)
                                                                                                       aaTAGCAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                    <  2:866199/139‑1 (MQ=255)
                                                                                                            cAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCCGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa                                                                         >  2:1089962/1‑81 (MQ=255)
                                                                                                            cAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       >  1:593322/1‑83 (MQ=255)
                                                                                                            cAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  2:593322/83‑1 (MQ=255)
                                                                                                            cAGAACATATCGCCGTTAAG‑CCATCACCC‑CCCCACTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa                                                                         <  1:1089962/81‑1 (MQ=255)
                                                                                                              gAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGatta             <  1:327169/139‑1 (MQ=255)
                                                                                                              gAACATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGatta             <  1:1279549/139‑1 (MQ=255)
                                                                                                                 cATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCTGGAATGGTTGAATTCCCCGcc                                  >  2:662779/1‑115 (MQ=255)
                                                                                                                 cATATCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  <  1:662779/115‑1 (MQ=255)
                                                                                                                    atCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  2:381222/75‑1 (MQ=255)
                                                                                                                    atCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       >  1:381222/1‑75 (MQ=255)
                                                                                                                    atCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTg                                             >  1:759660/1‑101 (MQ=255)
                                                                                                                    atCGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTg                                             <  2:759660/101‑1 (MQ=255)
                                                                                                                      cGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                              <  1:933190/114‑1 (MQ=255)
                                                                                                                      cGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                              <  1:1084962/114‑1 (MQ=255)
                                                                                                                      cGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                              >  2:933190/1‑114 (MQ=255)
                                                                                                                      cGCCGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                              >  2:1084962/1‑114 (MQ=255)
                                                                                                                         cGTTAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAc  <  2:563789/139‑1 (MQ=255)
                                                                                                                           ttAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                                  <  1:723117/73‑1 (MQ=255)
                                                                                                                           ttAAG‑CCATCACCC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                                  >  2:723117/1‑73 (MQ=255)
                                                                                                                                       |                                                                                                                              
AGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAG‑CCATCA‑CC‑CCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAC  >  NC_000913/1712379‑1712637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A