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
A5 F1 I1 R1	770	51.4	2439994	93.8%	2288714	110.3

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	92.0%	71.7 / 0.1	25	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 (14/9); total (15/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

CTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAT  >  NC_000913/4268353‑4268596

cTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑ttt‑tttttggg                                                                                                           <  2:1182491/139‑5 (MQ=255)

     gtcgCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAg                                                                                                       >  2:539501/1‑139 (MQ=255)

             cACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAAtt                                                                                               >  2:958953/1‑139 (MQ=255)

                 ctttctttATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTg                                                                                           <  1:958953/139‑1 (MQ=255)

                 ctttctttATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTg                                                                                           <  1:361942/139‑1 (MQ=255)

                 ctttctttATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTg                                                                                           <  1:539501/139‑1 (MQ=255)

                   ttctttATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGca                                                                                         <  2:76179/139‑1 (MQ=255)

                            gatgatTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTATTTTGGGTGGAGTAATAATTTCTg                                                                                           >  1:78807/1‑128 (MQ=255)

                            gatgatTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTATTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:78807/128‑1 (MQ=255)

                                atTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCatta                                                                            >  1:513654/1‑139 (MQ=255)

                                atTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCatta                                                                            >  2:672344/1‑139 (MQ=255)

                                atTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCatta                                                                            >  2:959317/1‑139 (MQ=255)

                                           gCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTg                                                                                           <  1:489388/113‑1 (MQ=255)

                                           gCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTg                                                                                           >  2:489388/1‑113 (MQ=255)

                                                    cTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCt                                                                                    >  1:153467/1‑111 (MQ=255)

                                                    cTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCt                                                                                    <  2:153467/111‑1 (MQ=255)

                                                                       cGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGaa                                     <  2:513654/139‑1 (MQ=255)

                                                                                     ttATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑ttt‑tttttggg                                                                                                           <  1:113741/54‑5 (MQ=255)

                                                                                     ttATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑ttt‑tttttggg                                                                                                           >  2:113741/1‑50 (MQ=255)

                                                                                      tATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:1134666/70‑1 (MQ=255)

                                                                                      tATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTg                                                                                           >  1:1134666/1‑70 (MQ=255)

                                                                                             aaGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAata               >  1:127261/1‑139 (MQ=255)

                                                                                                   aTCCCAACTATCTGGAATTCCTTCTCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATGTTTCTATATCCTCAAGAATATTCttt         >  1:1069365/1‑139 (MQ=255)

                                                                                                         aTTATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTa   >  1:975905/1‑139 (MQ=255)

                                                                                                          ttATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGTAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGc       >  2:1062200/1‑134 (MQ=255)

                                                                                                          ttATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGTAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGc       <  1:1062200/134‑1 (MQ=255)

                                                                                                          ttATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAt  >  1:807127/1‑139 (MQ=255)

                                                                                                          ttATCTGGAATTCCTTATCCTGTTTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAt  >  1:150825/1‑139 (MQ=255)

CTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTT‑TTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAT  >  NC_000913/4268353‑4268596

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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