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
A5 F1 I1 R1 81 47.9 2225048 94.8% 2109345 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,185,875 (G)7→6 intergenic (‑79/‑42) rcnR ← / → rcnA transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,185,8690G.100.0% 238.1 / NA 56intergenic (‑73/‑48)rcnR/rcnAtranscriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (32/24);  total (32/24)

ACCTGGCCCTGAATCTTACTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTGGGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCATGGCCT  >  NC_000913/2185732‑2186002
                                                                                                                                         |                                                                                                                                     
aCCTGGCCCTTAATCTTACTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTgg                                                                                                                                      <  2:807897/139‑1 (MQ=255)
      cccTGAATCTTACTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTggggggag                                                                                                                                >  1:167876/1‑137 (MQ=255)
           aaTCTTACTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGaa                                                                                                                          >  1:166761/1‑139 (MQ=255)
                     gCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTggg                                                                                                                                     <  2:453350/119‑1 (MQ=255)
                     gCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTggg                                                                                                                                     >  1:453350/1‑119 (MQ=255)
                     gCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGcc                                                                                                                >  2:910717/1‑139 (MQ=255)
                       aCGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGa                                                                                                              >  2:182994/1‑139 (MQ=255)
                       aCGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGa                                                                                                              >  2:1048485/1‑139 (MQ=255)
                        cgcgCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGaa                                                                                                             >  2:520088/1‑139 (MQ=255)
                         gcgcTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAAt                                                                                                            <  2:268368/139‑1 (MQ=255)
                                cAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACt                                                                                                     <  2:97313/139‑1 (MQ=255)
                                                cGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATg                                                                                     <  1:182994/139‑1 (MQ=255)
                                                   aTTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGc                                                                                                                 >  1:111165/1‑108 (MQ=255)
                                                   aTTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGc                                                                                                                 <  2:111165/108‑1 (MQ=255)
                                                   aTTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGAcc                                                                                  <  1:1048485/139‑1 (MQ=255)
                                                       tATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAAt                                                                              >  2:496133/1‑139 (MQ=255)
                                                         tGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAAttt                                                                            >  2:1068084/1‑139 (MQ=255)
                                                             aCATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACaa                                                                        <  2:326910/139‑1 (MQ=255)
                                                               aTGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTggg                                                                                                                                     <  1:1003697/77‑1 (MQ=255)
                                                               aTGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTggg                                                                                                                                     >  2:1003697/1‑77 (MQ=255)
                                                               aTGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTa                                                                                                    >  2:658248/1‑109 (MQ=255)
                                                               aTGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTa                                                                                                    <  1:658248/109‑1 (MQ=255)
                                                                 ggCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGa                                                                                >  1:554184/1‑127 (MQ=255)
                                                                 ggCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGa                                                                                <  2:554184/127‑1 (MQ=255)
                                                                 ggCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAActct                                                                    >  1:552152/1‑139 (MQ=255)
                                                                           ggTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGaa                                                                                                <  1:99303/101‑1 (MQ=255)
                                                                           ggTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGaa                                                                                                >  2:99303/1‑101 (MQ=255)
                                                                                 cAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCGGAATTAATATTAAGAATTATTTTCATGACCGAATTTACAACACTTATTCAGCAAGGaaaa                                                    >  2:832902/1‑138 (MQ=255)
                                                                                 cAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAAc                                                    >  2:537939/1‑139 (MQ=255)
                                                                                 cAAGAATATGAAAAATCATAGCACTATTAATCTACT‑GGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACg                                                   >  2:41274/1‑139 (MQ=255)
                                                                                   aGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGc                                                  <  1:496133/139‑1 (MQ=255)
                                                                                      atatGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGc                                                                                                                 <  1:312925/73‑1 (MQ=255)
                                                                                      atatGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGc                                                                                                                 >  2:312925/1‑73 (MQ=255)
                                                                                      atatGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTg                                               >  2:7458/1‑139 (MQ=255)
                                                                                                       acgaTTAATCTACTGGGGTGTAGTATCAGGTACT‑GGGGCGAGTAAAATCAGATTGCCGAATTACTACTAAGAATTATTATCATGTCCGAAATTACAACTCTTCTTCAGCAAGGAAACGGCTGGTTCTTCATCCCCAggg                              <  1:832902/136‑3 (MQ=255)
                                                                                                       aCTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAgcg                              <  2:552152/139‑1 (MQ=255)
                                                                                                           ttAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCAt                          >  2:784996/1‑139 (MQ=255)
                                                                                                           ttAATCTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCAt                          >  1:475537/1‑139 (MQ=255)
                                                                                                                cTACTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTAc                     <  1:910717/139‑1 (MQ=255)
                                                                                                                   cTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTaa                                                                                                   <  2:661899/58‑1 (MQ=255)
                                                                                                                   cTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTaa                                                                                                   >  1:661899/1‑58 (MQ=255)
                                                                                                                   cTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATccc                                   <  1:947659/122‑1 (MQ=255)
                                                                                                                   cTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATccc                                   >  2:947659/1‑122 (MQ=255)
                                                                                                                   cTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTg                  >  2:562873/1‑139 (MQ=255)
                                                                                                                   cTGGGGGGTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTg                  >  2:392871/1‑139 (MQ=255)
                                                                                                                     ggggggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACt                                                                                                     >  2:998725/1‑54 (MQ=255)
                                                                                                                     ggggggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACt                                                                                                     <  1:998725/54‑1 (MQ=255)
                                                                                                                     ggggggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTa                                                                                                    >  2:612575/1‑55 (MQ=255)
                                                                                                                     ggggggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTa                                                                                                    <  1:612575/55‑1 (MQ=255)
                                                                                                                     ggggggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATccc                                   >  2:540544/1‑120 (MQ=255)
                                                                                                                     ggggggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATccc                                   <  1:540544/120‑1 (MQ=255)
                                                                                                                     ggggggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTGCTTCATCCCCAGCGCCATCTTACTTGGt                >  2:665916/1‑139 (MQ=255)
                                                                                                                      gggggTAGTATCAGGTACT‑GGGGGGAGTAGAAGCAGATTGCCGAATTAATACTAAGAATTATTATCAGGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTg               >  1:349258/1‑139 (MQ=255)
                                                                                                                         ggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACt                                                                                                     <  2:315105/50‑1 (MQ=255)
                                                                                                                         ggTAGTATCAGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACt                                                                                                     >  1:315105/1‑50 (MQ=255)
                                                                                                                                  aGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGc                                                  >  2:147557/1‑92 (MQ=255)
                                                                                                                                  aGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGc                                                  <  1:147557/92‑1 (MQ=255)
                                                                                                                                  aGGTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCATGGcc   >  2:1042389/1‑139 (MQ=255)
                                                                                                                                   ggTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCa        >  2:53627/1‑133 (MQ=255)
                                                                                                                                   ggTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCa        <  1:53627/133‑1 (MQ=255)
                                                                                                                                   ggTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCATGGCCt  <  2:349258/139‑1 (MQ=255)
                                                                                                                                   ggTACT‑GGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCATGGCCt  <  1:1068084/139‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                     
ACCTGGCCCTGAATCTTACTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTGGGGGGGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATGACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCATGGCCT  >  NC_000913/2185732‑2186002

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