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
A13 F1 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,292,149	A→G	Y213C (TAC→TGC)	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,292,149	0	A	G	97.8%	151.6 / NA	45	Y213C (TAC→TGC)	nrfE	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (18/26); minor base T (1/0); total (19/26)
Fisher's exact test for biased strand distribution p-value = 4.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAGCGTGGCGCTGGCGAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTACTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCGCTGCTGCACAGTTTGTCCCTGACACGCCAGCGGGGGATTTTTTGCCACTGGT  >  NC_000913/4292020‑4292283

cgAGCGTGGCGCTGGCGAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACt                                                                                                                               >  2:794554/1‑139 (MQ=255)

  aGCGTGGCGCTGGCGAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCg                                                                                                                             >  1:1465136/1‑139 (MQ=255)

    cGTGGCGCTGGCGAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGc                                                                                                                           >  2:1110190/1‑139 (MQ=255)

         cgcTGGCGAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTgggg                                                                                                                      <  2:491111/139‑1 (MQ=255)

         cgcTGGCGAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTgggg                                                                                                                      <  2:600182/139‑1 (MQ=255)

               cGAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtg                                                                                                                <  2:390211/139‑1 (MQ=255)

                gAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtgg                                                                                                               <  1:1110190/139‑1 (MQ=255)

                gAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtgg                                                                                                               <  2:908953/139‑1 (MQ=255)

                gAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtgg                                                                                                               <  2:1465136/139‑1 (MQ=255)

                gAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtgg                                                                                                               <  1:679606/139‑1 (MQ=255)

                   tCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtggtgg                                                                                                            >  2:395348/1‑139 (MQ=255)

                        tGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATACTCGGTTCCTGGGGGGGCTGCTGCGAAATCGGGGGGGgggggtgggggtgttg                                                                                                       >  1:1208462/1‑135 (MQ=255)

                               cgAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCg                                                                                                >  2:521118/1‑139 (MQ=255)

                                gAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCgg                                                                                               <  2:573470/139‑1 (MQ=255)

                                       aTGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGaaaa                                                                                        <  2:243865/139‑1 (MQ=255)

                                       aTGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGaaaa                                                                                        <  2:1208462/139‑1 (MQ=255)

                                         ggTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACg                                                                                      >  1:1433252/1‑139 (MQ=255)

                                           tGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGcc                                                                                    <  1:521118/139‑1 (MQ=255)

                                           tGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGcc                                                                                    <  2:620275/139‑1 (MQ=255)

                                           tGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGcc                                                                                    >  2:250845/1‑139 (MQ=255)

                                           tGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTAGTTCTAGGATCCGGTGGAAAACGcc                                                                                    <  1:1376158/139‑1 (MQ=255)

                                                 cgcCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtggt                                                                                                              >  1:369269/1‑107 (MQ=255)

                                                 cgcCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtggt                                                                                                              <  2:369269/107‑1 (MQ=255)

                                                                  gcTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTgggg                                                                                                                      <  1:604550/82‑1 (MQ=255)

                                                                  gcTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTgggg                                                                                                                      >  2:604550/1‑82 (MQ=255)

                                                                           tACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCct                                                                                   <  1:587871/108‑1 (MQ=255)

                                                                           tACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCct                                                                                   >  2:587871/1‑108 (MQ=255)

                                                                             ccTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGACAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCgctgc                                                  <  2:981853/139‑1 (MQ=255)

                                                                                       gTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTTCTGCGAACTCGGCTgggg                                                                                                                      >  1:349259/1‑61 (MQ=255)

                                                                                       gTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTgggg                                                                                                                      <  2:349259/61‑1 (MQ=255)

                                                                                       gTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTtta                                                                              >  2:1390395/1‑101 (MQ=255)

                                                                                       gTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTtta                                                                              <  1:1390395/101‑1 (MQ=255)

                                                                                                  gcggGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtgg                                                                                                               >  1:1215518/1‑57 (MQ=255)

                                                                                                  gcggGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtgg                                                                                                               <  2:1215518/57‑1 (MQ=255)

                                                                                                   cggGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATcc                                                                                                 <  2:164137/70‑1 (MQ=255)

                                                                                                   cggGGATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGGGGTTCTGGGATcc                                                                                                 >  1:164137/1‑70 (MQ=255)

                                                                                                      ggATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGc                                                                                     <  2:1382575/79‑1 (MQ=255)

                                                                                                      ggATCATCCTCGGTTCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGc                                                                                     >  1:1382575/1‑79 (MQ=255)

                                                                                                                   ttCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtggtgg                                                                                                            >  1:729222/1‑43 (MQ=255)

                                                                                                                   ttCCTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCtggtgg                                                                                                            <  2:729222/43‑1 (MQ=255)

                                                                                                                     ccTGGTGGGCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCGCTGCTGCACAGTTTGTCCCTGACACGCCAGCGGGGGATTTTTTg          >  2:1609098/1‑139 (MQ=255)

                                                                                                                             gCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCGCTGCTGCACAGTTTGTCCCTGACACGCCAGCGGGGGATTTTTTGCCa       <  1:971255/134‑1 (MQ=255)

                                                                                                                             gCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCGCTGCTGCACAGTTTGTCCCTGACACGCCAGCGGGGGATTTTTTGCCa       >  2:971255/1‑134 (MQ=255)

                                                                                                                             gCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCGCTGCTGCACAGTTTGTCCCTGACACGCCAGCGGGGGATTTTTTGCCACTGGt  <  1:395348/139‑1 (MQ=255)

                                                                                                                             gCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCGCTGCTGCACAGTTTGTCCCTGACACGCCAGCGGGGGATTTTTTGCCACTGGt  <  1:1230096/139‑1 (MQ=255)

                                                                                                                             gCCTGCTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCGCTGCTGCACAGTTTGTCCCTGACACGCCAGCGGGGGATTTTTTGCCACTGGt  >  2:1230096/1‑139 (MQ=255)

CGAGCGTGGCGCTGGCGAGTCTACTGCGCGGCGAGTTTGATGGTGCCTGCGCCCGAATTTGCTGGCGCTGGGCGTTACCTGGCTGGAGTGCATTAACGGCGGGGATCATCCTCGGTTCCTGGTGGGCCTACTGCGAACTCGGCTGGGGCGGCTGGTGGTTCTGGGATCCGGTGGAAAACGCCTCTTTATTACCCTGGCTTTCTGCCACTGCGCTGCTGCACAGTTTGTCCCTGACACGCCAGCGGGGGATTTTTTGCCACTGGT  >  NC_000913/4292020‑4292283

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A