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
A12 F1 I1 R1	760	58.2	3022526	90.8%	2744453	102.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,268,487	(T)_7→8	intergenic (+180/+322)	tyrB → / ← yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,268,480	1	.	T	94.6%	111.3 / ‑0.5	37	intergenic (+173/+329)	tyrB/yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
Reads supporting (aligned to +/- strand): ref base . (1/1); new base T (18/17); total (19/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

GTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAT  >  NC_000913/4268355‑4268596

gtcgtcGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTg                                                                                                          <  1:1472803/139‑1 (MQ=255)

 tcgtcgCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATACCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTgg                                                                                                         >  2:951202/1‑139 (MQ=255)

                          gatgatTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑ttttttttggg                                                                                                           <  1:1173649/111‑5 (MQ=255)

                          gatgatTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑ttttttttggg                                                                                                           >  2:1173649/1‑107 (MQ=255)

                              atTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGATGGAGTAATAATTTCTGCACATCTAACCatta                                                                            >  1:689892/1‑139 (MQ=255)

                                ttttttGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGtaat                                                                                                   >  2:783488/1‑114 (MQ=255)

                                ttttttGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGtaat                                                                                                   <  1:783488/114‑1 (MQ=255)

                                     tGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGATGGAGTAATAATTTCTGCACATCTAACCATTATTAAAtt                                                                     <  2:689892/139‑1 (MQ=255)

                                                     cGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCgg                                                     >  2:1238130/1‑139 (MQ=255)

                                                           agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGa                                                                                                        <  2:1449207/82‑1 (MQ=255)

                                                           agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGa                                                                                                        >  1:1449207/1‑82 (MQ=255)

                                                           agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:70682/95‑1 (MQ=255)

                                                           agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           >  1:70682/1‑95 (MQ=255)

                                                           agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:1076675/95‑1 (MQ=255)

                                                           agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           >  1:1076675/1‑95 (MQ=255)

                                                           agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTtggg                                                                                                           >  1:520551/1‑77 (MQ=255)

                                                           agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTtggg                                                                                                           <  2:520551/78‑2 (MQ=255)

                                                                     cGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGaa                                     <  2:636736/139‑1 (MQ=255)

                                                                        tgttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  1:80615/82‑1 (MQ=255)

                                                                        tgttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           >  2:80615/1‑82 (MQ=255)

                                                                        tgttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAatat                                  >  2:381528/1‑139 (MQ=255)

                                                                          ttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           >  1:1477007/1‑80 (MQ=255)

                                                                          ttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:1477007/80‑1 (MQ=255)

                                                                            aGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCt                              >  1:706324/1‑139 (MQ=255)

                                                                                 ttttATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATc                         <  1:381528/139‑1 (MQ=255)

                                                                                  tttGTTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           >  2:970618/1‑72 (MQ=255)

                                                                                  tttATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  1:970618/72‑1 (MQ=255)

                                                                                   ttATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCt                       <  2:706324/139‑1 (MQ=255)

                                                                                                 aTCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:1240406/57‑1 (MQ=255)

                                                                                                 aTCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           >  1:1240406/1‑57 (MQ=255)

                                                                                                  tCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTAt                                                        <  2:1365060/91‑1 (MQ=255)

                                                                                                  tCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTAt                                                        >  1:1365060/1‑91 (MQ=255)

                                                                                                   cccAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaataa                                                               >  2:1209786/1‑83 (MQ=255)

                                                                                                   cccAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaataa                                                               <  1:1209786/83‑1 (MQ=255)

                                                                                                        ttATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAt  >  1:684607/1‑139 (MQ=255)

                                                                                                           tCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaataa                                                               >  2:1143439/1‑75 (MQ=255)

                                                                                                           tCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaataa                                                               <  1:1143439/75‑1 (MQ=255)

                                                                                                                       tATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGaa                 <  2:205155/109‑1 (MQ=255)

                                                                                                                       tATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGaa                 >  1:205155/1‑109 (MQ=255)

GTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAT  >  NC_000913/4268355‑4268596

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A