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
A20 F4 I5 R1	61	40.1	2005705	98.2%	1969602	131.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	AE015451_phaM1	5,681,415	+CGGG	intergenic (‑133/+71)	PP_4986 CDS (Channel protein_ hemolysin III family) ← / ← PP_4987 CDS (putative Chemotaxis protein)	–/–

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451_phaM1	= 5681415	0 (0.000)	13 (0.320) +CGGG	9/252	1.3	100%	intergenic (‑133/+71)	PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein)	–/–
*	?	AE015451_phaM1	5681416 =	0 (0.000)	13 (0.320) +CGGG	9/252	1.3	100%	intergenic (‑134/+70)	PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein)	–/–

AGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451_phaM1/5681301‑5681415

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAGGTCCGGTACCCGC  >  AE015451_phaM1/5681416‑5681555

                                                                                                                   ||||

AGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACA                                                                                                                     <  1:271999/144‑1

                                                           TGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAANCGCCGGGGATGCTGCGCAGACCTATCACGACACAAGGCCACTCCCCCCCCAGACCACCAAGCCCTGCGCCCCACACCCCCACCCAAGTCAG                                                          >  1:371042/1‑144

                                                           TGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGC                                                                                                            >  3:186641/1‑94

                                                           TGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGC                                                                                                            >  3:66772/1‑94

                                                                   AAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTCTCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGA                                                  >  1:9837/1‑144

                                                                   AAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCCGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGA                                                  >  1:9838/1‑144

                                                                           CGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCCGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTC                                          >  2:165270/1‑144

                                                                           CGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTC                                          >  2:165269/1‑144

                                                                              AGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCTAAGCACTATCTCGACCCAAGGCCGCTCCCCCCCCAAACCACCAGGCCCTGCGCCTCACATCCTCCCCAAGGTCAGGTTGCAGATCCGCGTCcc                                        >  5:47735/1‑141

                                                                                        GGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTCTCGCGACACAAGGCCGCTCCCACTCCCGACCACCCAGCCCTGCGCCTCACATCCTCACCAAGGTCAGGTTGCAGATCCGCATCACGCACCAGacct                             >  1:457145/1‑140

                                                                                                 TGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACACACCAGCCTTTCCAATGC                     >  5:40350/1‑143

                                                                                                          ATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAGGTC            >  6:19761/1‑143

                                                                                                            GAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAGGTCCG          >  6:73257/1‑143

                                                                                                                   CGGGGCTGCTGCGCAGCCCTATCGCGACACCAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGAACCAGCCTTTCCCCCGCGACCAGGTCCGGTACCCGC  >  1:109698/1‑144

                                                                                                                   CGGGGATGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCAACAGCCTTTCCAATGCGAACAGGTCCGGTACCCGC  >  1:109697/1‑144

                                                                                                                   ||||

AGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451_phaM1/5681301‑5681415

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAGGTCCGGTACCCGC  >  AE015451_phaM1/5681416‑5681555

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A