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 F44 I1 R1	56	64.5	2756482	98.4%	2712378	146.4

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	90.0%	21.2 / ‑3.1	10	intergenic (‑84/+87)	PP_4887/PP_4888	hypothetical protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand): ref base . (0/0); major base G (6/3); minor base T (1/0); total (7/3)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.74e-01
*	NC_002947_CJ‑RC	5,558,423	2	.	C	100.0%	29.6 / NA	10	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 (7/3); total (7/3)
*	NC_002947_CJ‑RC	5,558,423	3	.	C	100.0%	27.5 / NA	10	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 (7/3); total (7/3)

TTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG  >  NC_002947_CJ‑RC/5558296‑5558550

|||

ttCCGGGCGGCCTGGGCAGCTATTAGTCGGGCGTAAATGAGCAACTCCTTTTGTCATGGGGCGCCGACAGAATAGCAACACCGCTCTGGTGGGGGAGGGGCTTTGTGGCGCTAATGGGCCGATTAGCGGCCCCGGCAATTTCCGCgtgt                                                                                                               <  8:76839/149‑1 (MQ=255)

                 aGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCACTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg                                                                                              <  2:204400/149‑1 (MQ=255)

                                                                                           tgGGCGCGGCCTTGTGTCGCTAATGGGCCGAATCGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGc                    <  5:86768/149‑1 (MQ=37)

                                                                                                    ccTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCa           >  2:254109/1‑149 (MQ=255)

                                                                                                          gtCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCTAGTGTATGCAACAAAAATTGGGCTGCTATGAAGAGCTTTCACGACAAAAGGCCCACAAAGTACAGCGCAGGCTTAAGGACCCGAACTGGCCCAGGCTGGCGCGCCGCTGAg     >  4:69028/1‑149 (MQ=255)

                                                                                                           tCGCGAAAGGGCCGCATAGCGTCCCCGGCAATTTCCGCTTGTATGAAAAAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCACAAAAGGACCCCGCAGGCTTCAGGCCCGGAACTAGCCCAGGCTGGCGCGCAGcacagc    >  2:297206/1‑144 (MQ=25)

                                                                                                           tCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTg                            >  7:6764/1‑125 (MQ=38)

                                                                                                           tCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCAGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAACGCCCGCGCAGGCTTCAGGCCCGGCACTGGCCCAGGCTGGCGCGCAGCTgcgc    >  4:62985/1‑149 (MQ=38)

                                                                                                             gcgAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCAGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg  >  8:306075/1‑149 (MQ=39)

                                                                                                              cgAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGa      >  7:332084/1‑144 (MQ=255)

|||

TTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG  >  NC_002947_CJ‑RC/5558296‑5558550

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