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
A7 F1 I2 R1	766	64.2	3232166	90.9%	2938038	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,286,859	T→C	intergenic (+333/+207)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,286,859	0	T	C	100.0%	70.8 / NA	25	intergenic (+333/+207)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/13); total (12/13)

AAGCTTCTCATCCTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGA  >  NC_000913/1286810‑1286988

aaGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCgg                                          <  1:1337251/139‑1 (MQ=17)

  gCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGa                                                                                                       <  2:636131/76‑1 (MQ=11)

  gCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGa                                                                                                       >  1:636131/1‑76 (MQ=11)

   cTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCGTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCaa                                       <  1:871503/139‑1 (MQ=12)

              tCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCtt                                                           <  1:1448842/108‑1 (MQ=255)

              tCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCtt                                                           >  2:1448842/1‑108 (MQ=9)

                     atGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGaaa                                                                                                           >  2:7478/2‑53 (MQ=14)

                     atGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGaaa                                                                                                           <  1:7478/52‑1 (MQ=14)

                        ggCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTggggg                                                                                           >  2:723070/1‑66 (MQ=255)

                        ggCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTggggg                                                                                           <  1:723070/66‑1 (MQ=255)

                         gCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGAtggtgg                                                                                                 <  2:92236/59‑1 (MQ=255)

                         gCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGAtggtgg                                                                                                 >  1:92236/1‑59 (MQ=255)

                              atatTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGTCGaa            >  1:760428/1‑139 (MQ=16)

                                  ttGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTg                                                                                                        <  2:402171/43‑1 (MQ=255)

                                  ttGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTg                                                                                                        >  1:402171/1‑43 (MQ=255)

                                  ttGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGAtggtgg                                                                                                 >  2:542086/1‑50 (MQ=255)

                                  ttGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGAtggtgg                                                                                                 <  1:542086/50‑1 (MQ=255)

                                  ttGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCg                                                                >  2:1227181/1‑83 (MQ=255)

                                  ttGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCg                                                                <  1:1227181/83‑1 (MQ=255)

                                  ttGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCtt        >  2:1486158/1‑139 (MQ=255)

                                        gCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAATCGa  <  2:1348522/139‑1 (MQ=255)

                                         cGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTggggg                                                                                           <  1:771239/49‑1 (MQ=255)

                                         cGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTggggg                                                                                           >  2:771239/1‑49 (MQ=255)

                                         cGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCtt                                                           <  2:1502975/81‑1 (MQ=255)

                                         cGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCtt                                                           >  1:1502975/1‑81 (MQ=255)

AAGCTTCTCATCCTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGA  >  NC_000913/1286810‑1286988

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A