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 F1 I1 R1	150	26.0	2053212	90.0%	1847890	107.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	2,787,923	+C	intergenic (+165/‑55)	cafA2 → / → moaA1	Ribonuclease G and E/molybdopterin biosynthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	2,787,920	1	.	C	100.0%	29.3 / NA	9	intergenic (+162/‑58)	cafA2/moaA1	Ribonuclease G and E/molybdopterin biosynthesis protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (4/5); total (4/5)

ATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGA  >  AM260479/2787835‑2788032

aTGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGccca                                                                   <  2:999156/134‑1 (MQ=255)

                             ggTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTc                                      >  2:260654/1‑134 (MQ=255)

                                    cACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGAtttt                               <  2:324546/134‑1 (MQ=255)

                                                              cagAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTg                        <  1:688345/115‑1 (MQ=255)

                                                              cagAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTg                        >  2:688345/1‑115 (MQ=255)

                                                                    gCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCcaca                                                             <  1:562854/72‑1 (MQ=255)

                                                                    gCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCcaca                                                             >  2:562854/1‑72 (MQ=255)

                                                                         cGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGa  <  1:507327/126‑1 (MQ=255)

                                                                         cGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGa  >  2:507327/1‑126 (MQ=255)

ATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGA  >  AM260479/2787835‑2788032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `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

TCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCGGCAAGCTGGCTGCCCCCAC  >  AM260479/2787840‑2788069

cgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATC                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:2105:14271:44279/102‑1 (MQ=60)

                     acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACC                                                               <  GWNJ‑0478:712:GW2002102894th:2:2107:15208:59046/101‑1 (MQ=60)

                                     gacagCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTAC                                              <  GWNJ‑0478:712:GW2002102894th:2:2113:12925:34128/145‑1 (MQ=60)

                                                           GAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTC                        <  GWNJ‑0478:712:GW2002102894th:2:1216:8244:57348/150‑1 (MQ=60)

                                                                                C‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACtgtctcttatacacatctccgagcccacgagac  >  GWNJ‑0478:712:GW2002102894th:2:1103:3561:2792/1‑117 (MQ=60)

                                                                                C‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCGctgtctcttatacacatct  >  GWNJ‑0478:712:GW2002102894th:2:2212:17899:69457/1‑131 (MQ=60)

TCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCGGCAAGCTGGCTGCCCCCAC  >  AM260479/2787840‑2788069

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`