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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,950,559	(C)_5→6	intergenic (‑37/‑273)	aspS ← / → yecD	aspartyl‑tRNA synthetase/isochorismatase family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,950,554	1	.	C	96.5%	98.9 / ‑3.1	29	intergenic (‑32/‑278)	aspS/yecD	aspartyl‑tRNA synthetase/isochorismatase family protein
Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (15/13); total (15/14)
Fisher's exact test for biased strand distribution p-value = 4.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01

GAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑CCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTAC  >  NC_000913/1950418‑1950683

gAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑cc                                                                                                                                  >  1:758629/1‑139 (MQ=255)

      cAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑cccccctg                                                                                                                            <  1:679134/139‑4 (MQ=255)

                   tCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGAc                                                                                                               >  1:486615/1‑139 (MQ=255)

                    cACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGAcc                                                                                                              <  1:209131/139‑1 (MQ=255)

                       gacgacgGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAg                                                                                                           >  2:172103/1‑139 (MQ=255)

                            cgGTTGACCCAACCACACCGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTCTACGCAAGAGCTATACCTTAACTTAGCTGTCGGCGGATGACCCCC‑TGCTCCGCAGCTGACTAAGTAGCa                                                                                                      >  1:340782/1‑139 (MQ=255)

                              gTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCGGc                                                                                                    <  1:439961/139‑1 (MQ=255)

                                 gACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGtt                                                                                                 <  1:172103/139‑1 (MQ=255)

                                   cccAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAg                                                                                               <  2:486615/139‑1 (MQ=255)

                                      aaCCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTg                                                                                            <  1:234911/139‑1 (MQ=255)

                                                   cACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTa                                                                                          >  1:164796/1‑128 (MQ=255)

                                                   cACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTa                                                                                          <  2:164796/128‑1 (MQ=255)

                                                                                 cTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  >  2:22381/1‑122 (MQ=255)

                                                                                 cTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  <  1:22381/122‑1 (MQ=255)

                                                                                                tGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTa                                  <  2:758629/139‑1 (MQ=255)

                                                                                                       aTGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCt                           >  2:646574/1‑139 (MQ=255)

                                                                                                       aTGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCt                           >  2:301671/1‑139 (MQ=255)

                                                                                                       aTGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCt                           >  1:93874/1‑139 (MQ=255)

                                                                                                              atCCCTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCcgc                    >  1:405748/1‑139 (MQ=255)

                                                                                                                 ccTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAg                                                                                               <  2:322691/61‑1 (MQ=255)

                                                                                                                 ccTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAg                                                                                               >  1:322691/1‑61 (MQ=255)

                                                                                                                 ccTTAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCt                 >  2:404469/1‑139 (MQ=255)

                                                                                                                   ttAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTgg               <  2:572897/139‑1 (MQ=255)

                                                                                                                    tAACTTAGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGa              >  2:639747/1‑139 (MQ=255)

                                                                                                                          aGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCt        >  1:786804/1‑139 (MQ=255)

                                                                                                                          aGCTGCCGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCt        >  1:288128/1‑139 (MQ=255)

                                                                                                                               ccGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTa   >  1:492236/1‑139 (MQ=255)

                                                                                                                               ccGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTa   <  2:405748/139‑1 (MQ=255)

                                                                                                                               ccGGCGGATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTa   <  2:786804/139‑1 (MQ=255)

                                                                                                                                cggcggATG‑CCCCCGTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGTATGAAAAAAGGCGGCTATTATACTTGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTAc  <  2:492236/139‑1 (MQ=255)

                                                                                                                                 ggcggATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTa   >  1:512776/1‑137 (MQ=255)

                                                                                                                                 ggcggATGCCCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTa   <  2:512776/137‑1 (MQ=255)

GAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑CCCCC‑TGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTAC  >  NC_000913/1950418‑1950683

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 23 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A