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	3,475,701	T→C	S352P (TCG→CCG)	yheS →	ABC transporter ATP‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,475,701	0	T	C	90.9%	25.3 / ‑4.5	11	S352P (TCG→CCG)	yheS	ABC transporter ATP‑binding protein
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (6/4); total (6/5)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGC  >  NZ_CP009273/3475618‑3475781

aTCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAt                                                                            >  1:232881/1‑90 (MQ=255)

aTCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAt                                                                            >  1:82356/1‑90 (MQ=255)

                   gaTTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCgg                                                         <  1:325110/90‑1 (MQ=255)

                                      cccGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGc                                      >  1:321081/1‑90 (MQ=255)

                                                           ttAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGaaa                 <  2:229495/90‑1 (MQ=255)

                                                                  gCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTc                         >  1:263923/1‑75 (MQ=255)

                                                                  gCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTc                         <  2:263923/75‑1 (MQ=255)

                                                                    aaTGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCaaa        >  1:285297/1‑90 (MQ=255)

                                                                    aaTGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCaaa        >  2:127492/1‑90 (MQ=255)

                                                                          gcgGGTAAATCGCCATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGTAATTGGTCTGGCGAAAGGGATCCAACTCGGc  <  1:141860/90‑1 (MQ=255)

                                                                          gcgGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGc  <  2:41973/90‑1 (MQ=255)

ATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGC  >  NZ_CP009273/3475618‑3475781

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `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

GGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTCGCCCAGC  >  NZ_CP009273/3475608‑3475794

GGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAT                                                                                         >  SRR3722091.236482/1‑100 (MQ=60)

GGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAT                                                                                         >  SRR3722091.83632/1‑100 (MQ=60)

                             GATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCG                                                            <  SRR3722091.330740/100‑1 (MQ=60)

                                      GAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGC                                                   >  SRR3722091.326624/1‑100 (MQ=60)

                                                                  CTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGctgtc                       >  SRR3722091.268186/1‑95 (MQ=60)

                                                                    GTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAA                     >  SRR3722091.290061/1‑100 (MQ=60)

                                                                                    GCGGGTAAATCGCCATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGTAATTGGTCTGGCGAAAGGGATCCAACTCGGCTACTTCGCCC     <  SRR3722091.143962/100‑1 (MQ=60)

                                                                                       GGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCtgtctcttatacacat  >  SRR3722091.302809/1‑84 (MQ=60)

GGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTCGCCCAGC  >  NZ_CP009273/3475608‑3475794

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`