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 F14 I1 R1	58	76.7	3323998	98.6%	3277462	146.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947_CJ‑RC	5,558,423	+GCC	intergenic (‑84/+87)	PP_4887 ← / ← PP_4888	hypothetical protein/methyl‑accepting chemotaxis transducer

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	5,558,423	1	.	G	100.0%	26.4 / NA	11	intergenic (‑84/+87)	PP_4887/PP_4888	hypothetical protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (3/8); total (3/8)
*	NC_002947_CJ‑RC	5,558,423	2	.	C	100.0%	34.7 / NA	11	intergenic (‑84/+87)	PP_4887/PP_4888	hypothetical protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (3/8); total (3/8)
*	NC_002947_CJ‑RC	5,558,423	3	.	C	100.0%	34.1 / NA	11	intergenic (‑84/+87)	PP_4887/PP_4888	hypothetical protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (3/8); total (3/8)

CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC  >  NC_002947_CJ‑RC/5558276‑5558551

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cGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcg                                                                                                                                     <  2:220614/148‑1 (MQ=255)

                  aaTTCTGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAACGGGCCGCATAGCGGCCCCGGCAATTTCCGCgt                                                                                                                  <  6:405080/149‑1 (MQ=38)

                          gcgcccggggCTGCGATTCTTCGGGCGGACAGGAGCAACTCATTTTGTCATGTGTCCCCGACCGCATAGCAACCCCGCTCAGGGGTGGGAGGGGCCTTGTGTCGCTAAAGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGcaa                                                                                                          <  6:267691/142‑1 (MQ=255)

                             gCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCcgc                                                                                                                    <  4:305808/136‑1 (MQ=38)

                             gCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCcgc                                                                                                                    >  3:305808/1‑136 (MQ=38)

                               gggggCAGCTTTTTGTCGGGCGTAATTGAGCAACTCCTTTTGTCTTGTGGCGCCGACAGCATAGCAACACCGCTCAGGTGGGGGAGCGGCTTTGTGTCGCGAATGGGCCGAATCGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAAc                                                                                                     <  6:224579/147‑1 (MQ=255)

                                    cAGTGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGGCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTggg                                                                                                <  8:223988/149‑1 (MQ=38)

                                                gggCCGACATCAGCAACTCCTTTTGTCATGTGTCCCCGACAGCATAGCAACCCCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAg                                                                                    <  4:277669/149‑1 (MQ=37)

                                                         tGACCAACTCTTTTTGACCTGTGCCCCCCACACCAAACCACCCCCGCTGTGGGGGGGGTGCGGCCTTGTGCCCCTAATGGGCCGCATCGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc                                                                           <  6:66056/149‑1 (MQ=255)

                                                                                       cAGCATACCAACCCCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGc                                             <  8:309730/149‑1 (MQ=37)

                                                                                                                               tCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc     >  4:118463/1‑149 (MQ=255)

                                                                                                                                    aaaGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc  >  1:157309/1‑147 (MQ=255)

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CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC  >  NC_002947_CJ‑RC/5558276‑5558551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A