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
A1 F2 I231 R1	218	12.8	703680	97.2%	683976	86.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,812,807	(C)_7→8	intergenic (‑50/+55)	celF ← / ← chbR	6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,812,800	1	.	C	100.0%	27.0 / NA	10	intergenic (‑43/+62)	celF/chbR	6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (6/4); total (6/4)

GCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAT  >  NZ_CP009273/1812713‑1812883

gctgctCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cc                                                                                   <  2:15479/90‑1 (MQ=255)

        cGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccccccgg                                                                           <  1:225746/90‑4 (MQ=255)

                       cgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAg                                                             >  2:120158/1‑90 (MQ=255)

                                      ggCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGatat                                              >  2:198106/1‑90 (MQ=255)

                                                  ctcCCTTCAGTACAGAATGCTGATATCTGGCATATCGGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAg                                  <  1:253048/90‑1 (MQ=255)

                                                   tcCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAg                                  <  2:341966/90‑1 (MQ=255)

                                                                gAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAc                    <  2:123117/90‑1 (MQ=255)

                                                                gAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAc                    >  2:137650/1‑90 (MQ=255)

                                                                          atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt          >  2:181934/1‑90 (MQ=255)

                                                                            cTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCa        >  1:150426/1‑90 (MQ=255)

                                                                               gCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTc     >  1:302040/1‑90 (MQ=255)

                                                                                  tatCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAt  <  2:302040/90‑1 (MQ=255)

GCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAT  >  NZ_CP009273/1812713‑1812883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG  >  NZ_CP009273/1812721‑1812903

CGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAA                                                                                      <  SRR3722116.228763/100‑1 (MQ=60)

                                          CTCCCTTCAGTACAGAATGCTGATATCTGGCATATCGGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGAC                                            <  SRR3722116.256631/100‑1 (MQ=60)

                                                          ATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCA                            >  SRR3722116.152147/1‑100 (MQ=60)

                                                             CTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTC                         >  SRR3722116.306479/1‑100 (MQ=60)

                                                                                    CCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG  <  SRR3722116.244059/100‑1 (MQ=60)

CGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG  >  NZ_CP009273/1812721‑1812903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`