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 I1 R1	771	44.8	2153074	94.1%	2026042	109.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,291,201	C→T	G242G (GGC→GGT)	nrfD →	formate‑dependent nitrite reductase, membrane subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,291,201	0	C	T	85.3%	74.2 / 5.6	36	G242G (GGC→GGT)	nrfD	formate‑dependent nitrite reductase, membrane subunit
Reads supporting (aligned to +/- strand): ref base C (2/3); new base T (15/14); total (18/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CTGATCGCCATGGCGATACGCCAACGCAGTAACCCGCATTCCACGGAAGCGCAGTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGCGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCGGGCTGGGGCTGATTGTGCCAA  >  NC_000913/4291067‑4291301

cTGATCGCCATGGCGATACGCCAACGCAGTAACCCGCATTCCACGGAAGCGCAGTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGCGATg                                                                                                  <  1:866653/139‑1 (MQ=255)

               aTACGCCAACGCAGTAACCCGCATTCCACGGAAGCGCAGTTTGTACACCGTATGGAAATCCCTGAGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTg                                                                                   >  2:258243/1‑139 (MQ=255)

                 aCGCCAACGCAGTAACCCGCATTCCACGGAAGCGCAGTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGG‑GATGACGGTAAAGTTCGTgcgc                                                                                >  1:799742/1‑139 (MQ=255)

                       aCGCAGTAACCCGCATTCCACGGAAGCGCAGTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGCGATGACGGTAAAGTTCGTGCGCtggtg                                                                           >  1:186308/1‑139 (MQ=255)

                                  cGCATTCCACGGAAGCGCAGTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGG‑GATGACGGTAAAGTTCGTGCGATGGTGGCGGCATTAGGt                                                               <  2:799742/139‑1 (MQ=255)

                                    cATTCCACGGAAGCGCAGTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTg                                                              >  1:846209/1‑139 (MQ=255)

                                                     gTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACgtgg                                             <  2:846209/139‑1 (MQ=255)

                                                     gTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACgtgg                                             <  2:799298/139‑1 (MQ=255)

                                                          tACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGtt                                        <  1:73698/139‑1 (MQ=255)

                                                          tACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGtt                                        <  1:258243/139‑1 (MQ=255)

                                                                 tATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGtt                                        <  2:10765/132‑1 (MQ=255)

                                                                 tATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGtt                                        >  1:10765/1‑132 (MQ=255)

                                                                         tCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGtt                                        >  1:101363/1‑124 (MQ=255)

                                                                         tCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGtt                                        <  2:101363/124‑1 (MQ=255)

                                                                         tCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGc                         >  2:123057/1‑139 (MQ=255)

                                                                             tgtgGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGAt                                                                                                   >  2:589350/1‑61 (MQ=255)

                                                                             tgtgGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGAt                                                                                                   <  1:589350/61‑1 (MQ=255)

                                                                             tgtgGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGCGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCggg                     >  2:1070469/1‑139 (MQ=255)

                                                                                   aTGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGCGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggctgggg               <  2:186308/139‑1 (MQ=255)

                                                                                         tGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCg                                                           <  2:490264/89‑1 (MQ=255)

                                                                                         tGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCg                                                           >  1:490264/1‑89 (MQ=255)

                                                                                           aaaTCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCGGGCTGGGGCTGATtgt       >  2:190734/1‑139 (MQ=255)

                                                                                            aaTCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggctgggg               >  2:508590/1‑130 (MQ=255)

                                                                                            aaTCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggctgggg               <  1:508590/130‑1 (MQ=255)

                                                                                             aTCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGCGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCGGGCTGGGGCTGATTGTGc     <  1:1070469/139‑1 (MQ=255)

                                                                                                ttCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTAATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCGGGCTGGGGCTGATTGTGCCaa  >  2:239563/1‑139 (MQ=255)

                                                                                                 tCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGc                                                            >  2:123547/1‑80 (MQ=255)

                                                                                                 tCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGc                                                            <  1:123547/80‑1 (MQ=255)

                                                                                                     gctgGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGa                                                  >  1:988297/1‑86 (MQ=255)

                                                                                                     gctgGTGGCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGa                                                  <  2:988297/86‑1 (MQ=255)

                                                                                                          tggCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggctgggg               >  2:42297/1‑116 (MQ=255)

                                                                                                          tggCGTTTTTTGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggctgggg               <  1:42297/116‑1 (MQ=255)

                                                                                                                   ttGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggct                   >  1:915580/1‑103 (MQ=255)

                                                                                                                   ttGTCGGTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggct                   <  2:915580/103‑1 (MQ=255)

                                                                                                                         gTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggctgggg               <  1:89947/101‑1 (MQ=255)

                                                                                                                         gTCTGGCGCTGGGTGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCgggctgggg               >  2:89947/1‑101 (MQ=255)

CTGATCGCCATGGCGATACGCCAACGCAGTAACCCGCATTCCACGGAAGCGCAGTTTGTACACCGTATGGAAATCCCTGTGGTATGGGGTGAAATCTTCCTGCTGGTGGCGTTTTTTGTCGGTCTGGCGCTGGGCGATGACGGTAAAGTTCGTGCGCTGGTGGCGGCATTAGGTGGCGGTTTCTGGACGTGGTGGTTCTGGCTTGGTGTCGCCGGGCTGGGGCTGATTGTGCCAA  >  NC_000913/4291067‑4291301

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A