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 I209 R1	216	14.4	815930	96.1%	784108	85.2

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	91.7%	30.2 / ‑1.6	12	intergenic (‑43/+62)	celF/chbR	6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR
Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (6/5); total (6/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

GCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT  >  NZ_CP009273/1812716‑1812884

gctCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑ccccc                                                                                 >  1:194608/1‑90 (MQ=255)

                  gacgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATcc                                                                >  2:136746/1‑90 (MQ=255)

                        ttttAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAAc                                                          <  2:265513/90‑1 (MQ=255)

                            aaTTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc                                                     <  2:190125/90‑1 (MQ=255)

                             aTTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGAc                                                     <  1:148882/90‑1 (MQ=255)

                                              tctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCa                                    <  2:79469/90‑1 (MQ=255)

                                                   cTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGtat                               >  2:246746/1‑90 (MQ=255)

                                                              aaTACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACt                    <  1:136746/90‑1 (MQ=255)

                                                              aaTACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACt                    <  1:246746/90‑1 (MQ=255)

                                                                    gATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTaa              >  1:294142/1‑90 (MQ=255)

                                                                         cTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCa         >  1:379667/1‑90 (MQ=255)

                                                                              atatCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCaa    >  2:55653/1‑90 (MQ=255)

                                                                                atCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAtt  >  1:363990/1‑90 (MQ=255)

GCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT  >  NZ_CP009273/1812716‑1812884

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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

ATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT  >  NZ_CP009273/1812745‑1812884

ATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGA                                           <  SRR3722091.151079/100‑1 (MQ=60)

                             ACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAA              >  SRR3722091.299106/1‑100 (MQ=60)

                                 AATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTC          <  SRR3722091.138799/100‑1 (MQ=60)

                                 AATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTC          <  SRR3722091.250619/100‑1 (MQ=60)

                                  ATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCA         >  SRR3722091.386380/1‑100 (MQ=60)

                                         TATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT  >  SRR3722091.370393/1‑100 (MQ=60)

ATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT  >  NZ_CP009273/1812745‑1812884

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`