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 I227 R1	223	21.3	1167702	97.0%	1132670	86.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	476,525	A→G	intergenic (‑361/+185)	tomB ← / ← acrB	Hha toxicity modulator TomB/efflux RND transporter permease AcrB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	476,525	0	A	G	90.9%	24.3 / ‑3.1	11	intergenic (‑361/+185)	tomB/acrB	Hha toxicity modulator TomB/efflux RND transporter permease AcrB
Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (4/6); total (5/6)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.10e-01

AGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTT  >  NZ_CP009273/476439‑476610

aGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGgtta                                                                                    >  1:520366/1‑90 (MQ=255)

  gATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGgttatt                                                                                  >  2:539693/1‑90 (MQ=255)

      gCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAAt                                                                              >  2:242514/1‑90 (MQ=255)

                tGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAgcgc                                                                    <  1:121561/90‑1 (MQ=255)

                     taataaCCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACtt                                                               >  1:265790/1‑90 (MQ=255)

                                               tACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTAt                                     >  1:553994/1‑90 (MQ=255)

                                                                  tAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCg                  <  2:258975/90‑1 (MQ=255)

                                                                  tAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCg                  <  2:265790/90‑1 (MQ=255)

                                                                  tAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCg                  <  2:70346/90‑1 (MQ=255)

                                                                    gCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAAt                                           <  1:41137/63‑1 (MQ=255)

                                                                    gCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAAt                                           >  2:41137/1‑63 (MQ=255)

                                                                                  aTGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGttt  >  1:197811/1‑90 (MQ=255)

                                                                                  aTGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGttt  <  1:397306/90‑1 (MQ=255)

AGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTT  >  NZ_CP009273/476439‑476610

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TGACACTAATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTTTCGTATGAGA  >  NZ_CP009273/476426‑476620

TGACACTAATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGG                                                                                                 <  SRR3722111.466409/100‑1 (MQ=60)

   CACTAATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTA                                                                                              >  SRR3722111.528497/1‑100 (MQ=60)

                        GAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTT                                                                         >  SRR3722111.268981/1‑100 (MQ=60)

                             TGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATAT                                                                    <  SRR3722111.123085/100‑1 (MQ=60)

                                                  AATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTAT                                               >  SRR3722111.562704/1‑100 (MQ=60)

                                                      atgtgtataagagacagATTAAGAATAGCCTCTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTT                                           <  SRR3722111.41639/83‑1 (MQ=60)

                                                                                     CTAAATGATTATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTT            >  SRR3722111.200271/1‑100 (MQ=60)

                                                                                               ATGGGTTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTTTCGTATGAGA  <  SRR3722111.403071/100‑1 (MQ=60)

TGACACTAATACCAGGATTGCTCTGAATATGACGTAATAACCGAGGAATGAATAAAGAATTACCGCAAATAATTAAGAATAGCCTCTAAATGATTATGGATTATTAAATCTATTAGCGCTACTTAATATAAATTAACTAACAATCAGTATTTTTTATGAATTTTATCCGTGGTTAATACTGGTTTTCGTATGAGA  >  NZ_CP009273/476426‑476620

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`