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
A7 F1 I2 R1	766	64.2	3232166	90.9%	2938038	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	357,626	2 bp→TA	intergenic (+172/+164)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,626	0	C	T	100.0%	30.4 / NA	15	intergenic (+172/+165)	codA/cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (9/6); total (9/6)
*	NC_000913	357,627	0	C	A	93.3%	28.6 / ‑5.9	15	intergenic (+173/+164)	codA/cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (9/5); minor base T (0/1); total (9/6)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCA  >  NC_000913/357548‑357756

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cGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTg                                                                                   >  1:1233836/1‑128 (MQ=11)

cGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTg                                                                                   <  2:1233836/128‑1 (MQ=1)

cGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGcc                                                                        >  1:65965/1‑139 (MQ=255)

cGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGcc                                                                        >  2:1416697/1‑139 (MQ=255)

             cgtaTTCCGGACGATGATCTGTATCAGCGCTTCCTGTGATTCATTACCGGCCACATCCGTGCATTTTTACAACGCCATGTGCAAAAAGGCCTTCGCAGCGGCTTTCTGCCAGCTGTAGTTTATGCCGTATGCGGCGTgc                                                           <  1:578074/136‑2 (MQ=12)

                         gCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTATTTTATCCGCGACGCGGCGTGAACGCCTTATcgt                                               >  1:1461056/1‑137 (MQ=14)

                                  tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCATCGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTa                                      <  2:765947/139‑1 (MQ=18)

                                  tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTa                                      >  1:1000195/1‑139 (MQ=18)

                                  tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTa                                      >  1:1067287/1‑139 (MQ=18)

                                   gtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTag                                     <  1:589129/139‑1 (MQ=255)

                                            tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTg                                                            <  1:798362/107‑1 (MQ=255)

                                            tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTg                                                            >  2:798362/1‑107 (MQ=14)

                                             aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCATTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAAc                           >  2:1407775/1‑139 (MQ=255)

                                                              ccAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGc          >  1:758316/1‑139 (MQ=255)

                                                                      cgcgCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGCATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCa  <  2:1000195/139‑1 (MQ=255)

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CGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCA  >  NC_000913/357548‑357756

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A