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
A0 F0 I1 R1	149	26.7	2337422	87.5%	2045244	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	159,885	Δ1 bp	coding (149/939 nt)	h16_A0146 →	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	159,883	0	G	.	100.0%	16.1 / NA	5	coding (147/939 nt)	h16_A0146	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (3/2); total (3/2)

TCCCGGTGGATGTCAGCAACACGCCCACGCTGGAAGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCCGGGAACCCGCGCCGCAGGAAGCCCCCGCTCCCCCGCTCGCCACCAGCCCGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGC  >  AM260479/159753‑160013

tCCCGGTGGATGTCAGCAACACGCCCACGCTGGAAGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCCggaa                                                                                                                                 >  1:80269/1‑132 (MQ=255)

  ccGGTGGATGTCAGCAACACGCCCACGCTGGAAGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCCggaac                                                                                                                                <  2:80269/133‑4 (MQ=255)

                                                  ccgccCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAACCCGcgcc                                                                                                                        <  1:1085845/92‑1 (MQ=255)

                                                  ccgccCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAACCCGcgcc                                                                                                                        >  2:1085845/1‑92 (MQ=255)

                                                                               gcgGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAACCCGcgccgc                                                                                                                      <  1:497037/65‑1 (MQ=255)

                                                                               gcgGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAACCCGcgccgc                                                                                                                      >  2:497037/1‑65 (MQ=255)

                                                                               gcgGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAACCCGCGCCGCAGGAAGCCCCCGCTCCCCCGCTCGCCACCAGCCCGCAGGGCGCGACCGAGATGGCGTCGGGCAGTggcg                                                 >  2:881282/1‑134 (MQ=255)

                                                                                                                               ccccGGAACCCGCGCCGCAGGAAGCCCCCGCTCCCCCGCTCGCCACCAGCCCGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCcggc  >  2:313294/1‑134 (MQ=255)

TCCCGGTGGATGTCAGCAACACGCCCACGCTGGAAGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCCGGGAACCCGCGCCGCAGGAAGCCCCCGCTCCCCCGCTCGCCACCAGCCCGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGC  >  AM260479/159753‑160013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TGCCGGGGCCGCTGATCCCGGTGGATGTCAGCAACACGCCCACGCTGGAAGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCCGGGAACCCGCGCCGCAGGAAGCCCCCGCTCCCCCGCTCGCCACCAGCCC  >  AM260479/159738‑159931

TGCCGGGGCCGCTGATCCCGGTGGATGTCAGCAACACGCCCACGCTGGAAGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAAC                                             >  GWNJ‑0478:712:GW2002102894th:2:1107:18644:8751/1‑150 (MQ=60)

                       gggctcggagatgtgtataagagacagGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAACCCGCGCCGCAGGAAGCCCCCGC                       <  GWNJ‑0478:712:GW2002102894th:2:2213:17901:27587/122‑1 (MQ=60)

                        cggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAACCCGCGCCGCAGGAAGCCCCCGCTC                     <  GWNJ‑0478:712:GW2002102894th:2:1212:17117:34103/95‑1 (MQ=60)

                                           GCTGGAAGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCC‑GGAACCCGCGCCtgtctcttatacacatctccgagcccacgagacact  >  GWNJ‑0478:712:GW2002102894th:2:2211:8312:92408/1‑114 (MQ=60)

TGCCGGGGCCGCTGATCCCGGTGGATGTCAGCAACACGCCCACGCTGGAAGCGGTGCTGCTGCCGCCGCCCAGGCCGCCAGCCCCACCCGCGCCGCGGCCGGTGCCGCGCCCGCGCCCGCAGCCCAGGGCGGCCGCGCCGGCCCCGGGAACCCGCGCCGCAGGAAGCCCCCGCTCCCCCGCTCGCCACCAGCCC  >  AM260479/159738‑159931

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`