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
A8 F1 I2 R1	765	53.2	2691310	93.4%	2513683	103.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,301,599	G→A	G39S (GGC→AGC)	yhbU →	U32 peptidase family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,301,599	0	G	A	91.9%	94.6 / ‑0.1	37	G39S (GGC→AGC)	yhbU	U32 peptidase family protein
Reads supporting (aligned to +/- strand): ref base G (1/2); new base A (17/17); total (18/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GGAGCTGCTCTGCCCTGCCGGAAATCTCCCGGCGCTTAAGGCGGCC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCGGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTACGCCCGTTGGCAGCGCGCCGT  >  NC_000913/3301487‑3301726

ggAGCTGCTCTGCCCTGCCGGAAATCTCCCGGCGCTTAAGGCGGCC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTg                                                                                                       >  2:1066137/1‑139 (MQ=255)

     tgctCTGCCCTGCCGGAAATCTCCCGGCGCTTAAGGCGGCC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGa                                                                                                  <  1:23105/139‑1 (MQ=255)

       ctctGCCCTGCCGGAAATCTCCCGGCGCTTAAGGCGGCC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGc                                                                                                                               >  1:98051/1‑108 (MQ=255)

                gccGGAAATCTCCCGGCGCTTAAGGCGGCC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGtt                                                                                       <  1:1066137/139‑1 (MQ=255)

                 ccGGAAATCTCCCGGCGCTTAAGGCGGCC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTACCGGAAAAAAATTTCCAGAAAGCGTTAAGttt                                                                                      >  1:581682/1‑139 (MQ=255)

                   ggAAATTTCCCGGCGGTTTAGGCCGCCAATCGAAAACGG‑GGAAATGCTTGTTATTATCGGGTTAAAGGATGTTACCATTCCCCTTCACTTGCCAGGCCTT‑ACCTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTg                                                                                    <  2:581682/139‑1 (MQ=255)

                      aaTCTCCCGGCGCTTAAGGCGGCC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCGGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTcc                                                                                 >  1:1331292/1‑139 (MQ=255)

                                           gcC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTc                                                            <  1:1050199/139‑1 (MQ=255)

                                                    aaaCGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCGGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATcgcg                                                    <  2:1331292/139‑1 (MQ=255)

                                                                 gC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTg                                       <  1:628785/139‑1 (MQ=255)

                                                                     gTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGc                                                                                                      <  2:282981/73‑1 (MQ=255)

                                                                     gTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGc                                                                                                      >  1:282981/1‑73 (MQ=255)

                                                                          tatCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCg                               >  1:13095/1‑139 (MQ=255)

                                                                          tatCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGACCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCg                               >  1:890770/1‑139 (MQ=255)

                                                                              gggCTAAAAGATGGTACCAATGCCTGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGaa                                                                                                 <  2:951170/69‑1 (MQ=255)

                                                                              gggCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGaa                                                                                                 >  1:951170/1‑69 (MQ=255)

                                                                              gggCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATcg                                                      <  1:1216994/112‑1 (MQ=255)

                                                                              gggCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATcg                                                      >  2:1216994/1‑112 (MQ=255)

                                                                                gCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCa                                                                                                     >  1:26290/1‑63 (MQ=255)

                                                                                gCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCa                                                                                                     <  2:26290/63‑1 (MQ=255)

                                                                                gCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGt                         >  1:584162/1‑139 (MQ=255)

                                                                                gCTAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGt                         >  1:310527/1‑139 (MQ=255)

                                                                                  tAAAAGATGATACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTa                       <  2:584162/139‑1 (MQ=255)

                                                                                         tgatACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCAt                                  >  1:190730/1‑121 (MQ=255)

                                                                                         tgatACCAATGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCAt                                  <  2:190730/121‑1 (MQ=255)

                                                                                                aaTGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTACGCCCGTTGGCAgc         <  2:13095/139‑1 (MQ=255)

                                                                                                  tGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATcg                                                      >  1:85643/1‑92 (MQ=255)

                                                                                                  tGCCCGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATcg                                                      <  2:85643/92‑1 (MQ=255)

                                                                                                     ccGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTACGCCCGTTGGCAGCGCGcc    <  2:1315204/139‑1 (MQ=255)

                                                                                                     ccGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTACGCCCGTTGGCAGCGCGcc    <  2:310527/139‑1 (MQ=255)

                                                                                                      cGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTa                       <  2:415236/119‑1 (MQ=255)

                                                                                                      cGTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTa                       >  1:415236/1‑119 (MQ=255)

                                                                                                       gTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGaa                                                                                                 <  2:849730/44‑1 (MQ=255)

                                                                                                       gTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGaa                                                                                                 >  1:849730/1‑44 (MQ=255)

                                                                                                       gTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCaa                                                                 >  2:1201440/1‑76 (MQ=255)

                                                                                                       gTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCaa                                                                 <  1:1201440/76‑1 (MQ=255)

                                                                                                       gTCACTTCGCCAGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTACGCCCGTTGGCAGCGCGCCGt  >  2:71156/1‑139 (MQ=255)

GGAGCTGCTCTGCCCTGCCGGAAATCTCCCGGCGCTTAAGGCGGCC‑ATCGAAAACGGCGCAGATGC‑TGTTTATATCGGGCTAAAAGATGATACCAATGCCCGTCACTTCGCCGGCCTTAACTTTACCGAGAAAAAATTGCAGGAAGCGGTGAGTTTTGTCCATCAACATCGCCGCAAACTTCACATCGCGATTAACACTTTTGCGCATCCGGACGGTTACGCCCGTTGGCAGCGCGCCGT  >  NC_000913/3301487‑3301726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `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