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
A11 F212 I1 R1	174	80.0	3892211	96.7%	3763768	99.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,289,526	A→G	K94K (AAA→AAG)	nrfB →	nitrite reductase, formate‑dependent, penta‑heme cytochrome c

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,289,526	0	A	G	96.1%	260.3 / ‑0.0	77	K94K (AAA→AAG)	nrfB	nitrite reductase, formate‑dependent, penta‑heme cytochrome c
Reads supporting (aligned to +/- strand): ref base A (1/2); new base G (44/30); total (45/32)
Fisher's exact test for biased strand distribution p-value = 5.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

AAAACATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAAGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCAAAAAGCG  >  NC_000913/4289430‑4289619

aaaaCATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGAt                                                                                            >  1:344386/1‑100 (MQ=255)

aaaaCATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGAt                                                                                            >  1:1606320/1‑100 (MQ=255)

      tGCTTCCGTTATCTACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATg                                                                                      >  2:1321522/1‑100 (MQ=255)

      tGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATg                                                                                      <  2:290818/100‑1 (MQ=255)

       gCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGGCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATgc                                                                                     <  1:881199/100‑1 (MQ=255)

        cTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATgcg                                                                                    >  1:1320791/1‑100 (MQ=255)

         ttCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATgcgc                                                                                   >  2:999335/1‑100 (MQ=255)

          tCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAAGATGTGATGCGCt                                                                                  <  2:656834/100‑1 (MQ=255)

           ccGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCtt                                                                                 <  2:990429/100‑1 (MQ=255)

              ttATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTaa                                                                              >  2:1084498/1‑100 (MQ=255)

              ttATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTaa                                                                              <  1:852926/100‑1 (MQ=255)

               tATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAAc                                                                             <  2:308590/100‑1 (MQ=255)

                aTCCACCCGAATAACAAACTGCCGGTCACCTGCACCGACTTGCAGGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAAGATGTGATGCGCTTTAAc                                                                             <  1:1903011/99‑1 (MQ=255)

                 tCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGa                                                                           >  2:1019205/1‑100 (MQ=255)

                  cAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATgcgtcttcatcca                                                                          >  1:1935034/1‑90 (MQ=255)

                    aCCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGcc                                                                        >  2:43596/1‑100 (MQ=255)

                    aCCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGcc                                                                        >  2:1708571/1‑100 (MQ=255)

                     cccGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCg                                                                       >  1:1583222/1‑100 (MQ=255)

                     cccGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCg                                                                       >  2:1766987/1‑100 (MQ=255)

                     cccGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCg                                                                       >  1:1322522/1‑100 (MQ=255)

                           tAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTAc                                                                 >  2:800113/1‑100 (MQ=255)

                             aCAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACaa                                                               >  1:1174818/1‑100 (MQ=255)

                             aCAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACaa                                                               >  2:1656896/1‑100 (MQ=255)

                             aCAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACaa                                                               >  2:1656327/1‑100 (MQ=255)

                             aCAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACaa                                                               >  2:1113850/1‑100 (MQ=255)

                              cAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAg                                                              <  2:634893/100‑1 (MQ=255)

                              cAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCCTTAACGAGCCGATGTACAAg                                                              <  2:1826474/100‑1 (MQ=255)

                               aaaCTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACGAgg                                                             >  1:519764/1‑100 (MQ=255)

                                aaCTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAgg                                                             >  1:326624/1‑99 (MQ=255)

                                  cTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTg                                                          >  2:1148698/1‑100 (MQ=255)

                                    gCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGga                                                        >  2:183201/1‑100 (MQ=255)

                                    gCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGga                                                        >  2:1587750/1‑100 (MQ=255)

                                     ccGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGgag                                                       <  2:447532/100‑1 (MQ=255)

                                     ccGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGgag                                                       <  1:838635/100‑1 (MQ=255)

                                        gTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAgcgc                                                    >  2:1935049/1‑100 (MQ=255)

                                        gTCACCTGCACCAACTCTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGc                                                    <  1:1137579/100‑1 (MQ=255)

                                          cACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAg                                                  <  2:1087752/100‑1 (MQ=255)

                                              tGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTCGGAGAGCAGAACa                                              <  2:1320798/100‑1 (MQ=255)

                                               gCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAg                                             <  2:1201677/100‑1 (MQ=255)

                                                 aCCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCg                                           >  1:933606/1‑100 (MQ=255)

                                                  ccAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGt                                          >  2:1122337/1‑100 (MQ=255)

                                                    aaCTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCt                                        >  1:1225479/1‑100 (MQ=255)

                                                      cTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGt                                      <  1:919619/100‑1 (MQ=255)

                                                       tGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTa                                     >  1:442310/1‑100 (MQ=255)

                                                       tGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTa                                     <  2:514727/100‑1 (MQ=255)

                                                       tGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTa                                     <  1:999334/100‑1 (MQ=255)

                                                        gTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTAt                                    >  2:1490228/1‑100 (MQ=255)

                                                        gTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTAt                                    >  2:1616201/1‑100 (MQ=255)

                                                          cACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGt                                  >  1:422840/1‑100 (MQ=255)

                                                          cACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGt                                  <  1:1238965/100‑1 (MQ=255)

                                                            cGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTcc                                >  2:478106/1‑100 (MQ=255)

                                                            cGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTcc                                >  2:9762/1‑100 (MQ=255)

                                                             ggCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCt                               <  1:1601658/100‑1 (MQ=255)

                                                              gccagccaTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCTTCTGTATGTCCTg                              <  2:1310975/100‑1 (MQ=255)

                                                              gccagccaTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTg                              <  1:449839/100‑1 (MQ=255)

                                                              gccagccaTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTg                              >  1:1378605/1‑100 (MQ=255)

                                                                 agccaTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCa                           <  1:626883/100‑1 (MQ=255)

                                                                   ccaTCACCGCAACACGGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGCGCCGATGTACCAGGTTGGAGAGCAGACCAGCGTCTGTATGCCCTGt                             <  1:1859672/96‑1 (MQ=255)

                                                                    caTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCt                        <  1:1271204/100‑1 (MQ=255)

                                                                    caTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCt                        <  2:215391/100‑1 (MQ=255)

                                                                     aTCACCGCAACACCGCGAAGGGGTGAAAGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTg                       >  2:251732/1‑100 (MQ=255)

                                                                      tCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCCATGTACAAGGTTGGAGAGCAGAACAGCGCCTGTCTGTCCTGTCATCTGc                      >  1:55807/1‑100 (MQ=255)

                                                                       cACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGcc                     >  2:1211569/1‑100 (MQ=255)

                                                                         ccGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCgg                   <  1:9762/100‑1 (MQ=255)

                                                                          cGCAACACGGCGAAGGGGTGAAGGGTGTGATGCGCGTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGGCTGTATGGCCTGTCAGCTGcc                     <  1:448207/97‑1 (MQ=255)

                                                                           gCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGaa                 <  2:1225482/100‑1 (MQ=255)

                                                                            cAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAAc                >  1:1352118/1‑100 (MQ=255)

                                                                              acacCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAg              >  2:161643/1‑100 (MQ=255)

                                                                              acacCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAg              <  1:293807/100‑1 (MQ=255)

                                                                              acacCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAg              >  1:650510/1‑100 (MQ=255)

                                                                                acCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGtt            <  2:830880/100‑1 (MQ=255)

                                                                                 ccGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTg           >  1:1676497/1‑100 (MQ=255)

                                                                                   gcgAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCa         <  2:1174820/100‑1 (MQ=255)

                                                                                   gcgAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCa         >  1:791613/1‑100 (MQ=255)

                                                                                      aaGGGGTG‑AGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCaaaaa     >  1:543261/1‑100 (MQ=255)

                                                                                        ggggTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCAAAAAg    >  2:1507333/1‑100 (MQ=255)

                                                                                          ggTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCAAAAAGCg  >  1:1552170/1‑100 (MQ=255)

AAAACATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAAGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCAAAAAGCG  >  NC_000913/4289430‑4289619

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A