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
A9 F1 I1 R1	64	69.7	3300380	93.4%	3082554	111.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,293,898	A→G	Y119C (TAC→TGC)	nrfG →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,293,898	0	A	G	83.1%	168.5 / 19.6	65	Y119C (TAC→TGC)	nrfG	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG
Reads supporting (aligned to +/- strand): ref base A (7/4); new base G (30/24); total (37/28)
Fisher's exact test for biased strand distribution p-value = 7.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAACAGTGGGCGTTACTGGGCGAGTACTATCTGTGGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACTACGCGCAAGCCAT  >  NC_000913/4293761‑4294033

cGAACAGTGGGCGTTACTGGGCGAGTACTATCTGTGGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTAc                                                                                                                                        >  2:1210816/1‑139 (MQ=255)

      aggggCGTTACTGGGCGAGTACTATCTGTGGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCCTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACCGTATGCGGCGCTGGCGACGGTACTTTATTGCCAGgcc                                                                                                                                  <  1:1102319/137‑1 (MQ=255)

          gCGTTACTGGGCGAGTACTATCTGTGGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGgccagcc                                                                                                                              >  1:1407140/1‑139 (MQ=255)

                   ggCGAGTACTATCTGTGGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGa                                                                                                                     <  2:1400407/139‑1 (MQ=255)

                   ggCGAGTACTATCTGTGGCAAAACGATTAAAGCAATTAGTTGCGGGCGTACCGTCAGGCGTTGCAACTACGTGGAGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGTCCAGCCAGCatatct                                                                                                                     >  2:1102319/1‑137 (MQ=255)

                    gCGAGTACTATCTGTGGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGAc                                                                                                                    >  2:1317311/1‑139 (MQ=255)

                          aCTATCTGTGGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCa                                                                                                              <  2:1342498/139‑1 (MQ=255)

                                  tgGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCatat                                                                                                                       <  1:617247/122‑1 (MQ=255)

                                  tgGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCatat                                                                                                                       >  2:617247/1‑122 (MQ=255)

                                  tgGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTcgcg                                                                                                      >  2:200062/1‑139 (MQ=255)

                                  tgGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTcgcg                                                                                                      <  2:1151393/139‑1 (MQ=255)

                                  tgGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTcgcg                                                                                                      >  1:327219/1‑139 (MQ=255)

                                   ggCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCgcgc                                                                                                     >  2:592472/1‑139 (MQ=255)

                                   ggCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCgcgc                                                                                                     >  1:790691/1‑139 (MQ=255)

                                     cAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCaa                                                                                                   >  1:1283642/1‑139 (MQ=255)

                                        aaCGATTACAGCAATTCGTTGCTGTCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGa                                                                                                <  2:920488/139‑1 (MQ=255)

                                        aaCGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGa                                                                                                >  1:298392/1‑139 (MQ=255)

                                        aaCGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGa                                                                                                >  2:890925/1‑139 (MQ=255)

                                                    aaTTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGccc                                                                                    <  2:1407140/139‑1 (MQ=255)

                                                            gCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTg                                                                            <  1:556357/139‑1 (MQ=255)

                                                               ggCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGAc                                                                         <  1:1210816/139‑1 (MQ=255)

                                                                   tACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTa                                                                     >  1:1392478/1‑139 (MQ=255)

                                                                     ccGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAAt                                                                   >  2:116374/1‑139 (MQ=255)

                                                                     ccGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAAt                                                                   >  2:917598/1‑139 (MQ=255)

                                                                       gTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGa                                                                 >  2:962825/1‑139 (MQ=255)

                                                                          aGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACa                                                                        >  1:642174/1‑129 (MQ=255)

                                                                          aGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACa                                                                        <  2:642174/129‑1 (MQ=255)

                                                                          aGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAAt                                                              >  2:431695/1‑139 (MQ=255)

                                                                                 gCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGcc                                                       >  2:965652/1‑139 (MQ=255)

                                                                                          tggtgAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGcc                                                                                                                <  1:550880/73‑1 (MQ=255)

                                                                                          tggtgAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGcc                                                                                                                >  2:550880/1‑73 (MQ=255)

                                                                                               agaACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGc                                         <  1:962825/139‑1 (MQ=255)

                                                                                                 aaCGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGcc                                                                                                                                       >  2:965838/1‑43 (MQ=255)

                                                                                                 aaCGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGcc                                                                                                                                       <  1:965838/43‑1 (MQ=255)

                                                                                                 aaCGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCtt                                       >  1:1376112/1‑139 (MQ=255)

                                                                                                     cTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTg                                                                            <  1:1641117/98‑1 (MQ=255)

                                                                                                     cTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTg                                                                            >  2:1641117/1‑98 (MQ=255)

                                                                                                       gAACTGTATGCGGCGCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGAc                                                                                                           >  1:324741/1‑65 (MQ=255)

                                                                                                       gAACTGTATGCGGCGCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGAc                                                                                                           <  2:324741/65‑1 (MQ=255)

                                                                                                         aCTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCg                               <  1:890925/139‑1 (MQ=255)

                                                                                                         aCTGTATGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCg                               >  1:623292/1‑139 (MQ=255)

                                                                                                              aTGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTcgcg                                                                               >  1:305386/1‑86 (MQ=255)

                                                                                                              aTGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTcgcg                                                                               <  2:305386/86‑1 (MQ=255)

                                                                                                               tGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATgctgct                                            >  1:15266/1‑120 (MQ=255)

                                                                                                               tGCGGCGCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATgctgct                                            <  2:15266/120‑1 (MQ=255)

                                                                                                                  ggcgCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGAtgctg                                              <  2:886944/115‑1 (MQ=255)

                                                                                                                  ggcgCTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGAtgctg                                              >  1:886944/1‑115 (MQ=255)

                                                                                                                  ggcgCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGAc                                                                                                           >  2:1268299/1‑54 (MQ=255)

                                                                                                                  ggcgCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGACTcgcg                                                                                                      <  2:80895/59‑1 (MQ=255)

                                                                                                                  ggcgCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGACTcgcg                                                                                                      >  1:80895/1‑59 (MQ=255)

                                                                                                                  ggcgCTGGCGACGGTGCTGTATTACCAGGCCAGCCAGCATATGACCGCCCAGAc                                                                                                           <  1:1268299/54‑1 (MQ=255)

                                                                                                                     gcTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGAc                                                                                                           >  1:11552/1‑51 (MQ=255)

                                                                                                                     gcTGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGAc                                                                                                           <  2:11552/51‑1 (MQ=255)

                                                                                                                       tGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGa                                                                          <  1:1539724/82‑1 (MQ=255)

                                                                                                                       tGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGa                                                                          >  2:1539724/1‑82 (MQ=255)

                                                                                                                       tGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGaa                 >  2:1398544/1‑139 (MQ=255)

                                                                                                                       tGGCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGaa                 >  2:1232595/1‑139 (MQ=255)

                                                                                                                        ggCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAAc                <  1:426706/139‑1 (MQ=255)

                                                                                                                         gCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACt               <  1:592472/139‑1 (MQ=255)

                                                                                                                         gCGACGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACt               <  2:790691/139‑1 (MQ=255)

                                                                                                                            aCGGTGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACTAcg            >  2:350249/1‑139 (MQ=255)

                                                                                                                                tGCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACTACGCGCa        <  1:116374/139‑1 (MQ=255)

                                                                                                                                 gCTTTATTGCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACTACGCGCaa       <  2:298392/139‑1 (MQ=255)

                                                                                                                                   tttATTACCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACTACGCGCAAGc     >  2:518192/1‑139 (MQ=255)

                                                                                                                                   tttATTACCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACTACGCGCAAGc     >  2:1631715/1‑139 (MQ=255)

                                                                                                                                      attgCCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACTACGCGCAAGCCAt  <  2:1043109/139‑1 (MQ=255)

CGAACAGTGGGCGTTACTGGGCGAGTACTATCTGTGGCAAAACGATTACAGCAATTCGTTGCTGGCGTACCGTCAGGCGTTGCAACTACGTGGTGAGAACGCTGAACTGTATGCGGCGCTGGCGACGGTGCTTTATTACCAGGCCAGCCAGCATATGACCGCCCAGACTCGCGCAATGATCGACAAAGCCCTCGCGCTGGACAGTAATGAAATCACCGCCCTGATGCTGCTGGCTTCCGATGCGTTTATGCAGGCGAACTACGCGCAAGCCAT  >  NC_000913/4293761‑4294033

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