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
A12 F1 I1 R1	760	58.2	3022526	90.8%	2744453	102.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	586,280	T→C	N210S (AAC→AGC)	envY ←	porin thermoregulatory transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	586,280	0	T	C	100.0%	129.3 / NA	36	N210S (AAC→AGC)	envY	porin thermoregulatory transcriptional activator
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (18/18); total (18/18)

CCTTCACCACATCACTTTTTGTCGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGTTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTGG  >  NC_000913/586144‑586382

ccTTCACCTCATCACTTTTTGTCGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGTGTGATATTTTTGCTa                                                                                                      <  2:684952/139‑1 (MQ=255)

                      cGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACgg                                                                                >  2:411756/1‑139 (MQ=255)

                         tGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGt                                                                             >  2:133234/1‑139 (MQ=255)

                                     tAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAACTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAATGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACACATACGac                                                                 >  1:325867/1‑139 (MQ=255)

                                            aCGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCtgt                                                          >  1:436239/1‑139 (MQ=255)

                                                  tCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAAt                                                    <  1:133234/139‑1 (MQ=255)

                                                          tAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAAt                                                                                             <  2:614711/90‑1 (MQ=255)

                                                          tAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAAt                                                                                             >  1:614711/1‑90 (MQ=255)

                                                                  cTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTa                                    >  1:1297265/1‑139 (MQ=255)

                                                                                       cgacgTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAAt                                                                                             <  1:12568/61‑1 (MQ=255)

                                                                                       cgacgTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAAt                                                                                             >  2:12568/1‑61 (MQ=255)

                                                                                         acgTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCttttt             >  1:273057/1‑139 (MQ=255)

                                                                                          cgTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCa                                                                                                  >  2:610480/1‑53 (MQ=255)

                                                                                          cgTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCa                                                                                                  <  1:610480/53‑1 (MQ=255)

                                                                                            tgctgcTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAg          <  2:273057/139‑1 (MQ=255)

                                                                                             gctgctATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGc                                               >  2:788438/1‑101 (MQ=255)

                                                                                             gctgctATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGc                                               <  1:788438/101‑1 (MQ=255)

                                                                                             gctgctATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGc         >  2:1247284/1‑139 (MQ=255)

                                                                                              ctgctATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCa        >  1:1152559/1‑139 (MQ=255)

                                                                                                  tataGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt    <  2:436239/139‑1 (MQ=255)

                                                                                                  tataGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt    <  2:1152559/139‑1 (MQ=255)

                                                                                                  tataGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt    <  1:1247284/139‑1 (MQ=255)

                                                                                                    taGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTgg  <  2:1297265/139‑1 (MQ=255)

                                                                                                    taGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTgg  <  1:411756/139‑1 (MQ=255)

                                                                                                           aTAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt    <  1:530123/130‑1 (MQ=255)

                                                                                                           aTAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt    >  2:530123/1‑130 (MQ=255)

                                                                                                                    ccACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAg          >  2:404009/1‑115 (MQ=255)

                                                                                                                    ccACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAg          <  1:404009/115‑1 (MQ=255)

                                                                                                                       ccTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGcg    >  2:195162/1‑117 (MQ=255)

                                                                                                                       ccTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt    <  1:195162/118‑1 (MQ=255)

                                                                                                                           aGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt    >  1:755546/1‑114 (MQ=255)

                                                                                                                           aGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt    <  2:755546/114‑1 (MQ=255)

                                                                                                                                 atTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAAt                                                    >  1:508029/1‑60 (MQ=255)

                                                                                                                                 atTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAAt                                                    <  2:508029/60‑1 (MQ=255)

                                                                                                                                  tttttGCTATCCATCAATAACATCTGTACGGCGTa                                                                            >  2:230089/1‑35 (MQ=255)

                                                                                                                                  tttttGCTATCCATCAATAACATCTGTACGGCGTa                                                                            <  1:230089/35‑1 (MQ=255)

CCTTCACCACATCACTTTTTGTCGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGTTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTGG  >  NC_000913/586144‑586382

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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