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
A13 F1 I2 R1	762	35.5	1545288	95.5%	1475750	117.0

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	92.6%	78.1 / ‑0.1	27	intergenic (+173/+329)	tyrB/yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
Reads supporting (aligned to +/- strand): ref base . (2/0); new base T (9/16); total (11/16)
Fisher's exact test for biased strand distribution p-value = 1.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.62e-01

CTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAT  >  NC_000913/4268353‑4268596

cTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑tttt‑tt‑ttggg                                                                                                           <  2:333126/139‑5 (MQ=255)

   tcgtcgCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTgg                                                                                                         >  2:438956/1‑139 (MQ=255)

   tcgtcgCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTCTT‑TGGGttg                                                                                                         >  2:455385/1‑137 (MQ=255)

         cTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATTGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGtaat                                                                                                   <  1:422565/139‑1 (MQ=255)

                 ctttctttATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTg                                                                                           <  2:89103/139‑1 (MQ=255)

                 ctttctttATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTg                                                                                           <  2:744012/139‑1 (MQ=255)

                 ctttctttATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTCAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTg                                                                                           <  2:471828/139‑1 (MQ=255)

                        tataGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCt                                                                                    <  2:9553/139‑1 (MQ=255)

                           aGATGATTTTTTTGTTGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAAc                                                                                 <  2:649233/139‑1 (MQ=255)

                           aGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAAc                                                                                 <  1:411172/139‑1 (MQ=255)

                                    ttttGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTT‑TTGTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTaa                                                                        >  2:486552/1‑139 (MQ=255)

                                              aTCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaataat                                                              <  2:340281/139‑1 (MQ=255)

                                                               ataataAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCt                                                                                    <  1:546740/100‑1 (MQ=255)

                                                               ataataAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCt                                                                                    >  2:546740/1‑100 (MQ=255)

                                                                       cGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGaa                                     <  1:486552/139‑1 (MQ=255)

                                                                           gttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTAt                                                        >  1:678162/1‑116 (MQ=255)

                                                                           gttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTAt                                                        <  2:678162/116‑1 (MQ=255)

                                                                                 tCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCtata                           <  2:38089/139‑1 (MQ=255)

                                                                                             aaGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGc                                                                                          >  1:728330/1‑64 (MQ=255)

                                                                                             aaGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGc                                                                                          <  2:728330/64‑1 (MQ=255)

                                                                                                 ttATCCCAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCt           <  1:643356/139‑1 (MQ=255)

                                                                                                     cccAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAata                                   >  2:123607/1‑111 (MQ=255)

                                                                                                     cccAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAata                                   <  1:123607/111‑1 (MQ=255)

                                                                                                     cccAATTATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGc       >  1:161346/1‑139 (MQ=255)

                                                                                                          ttATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAAtt                                                                     >  2:452359/1‑72 (MQ=255)

                                                                                                          ttATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAAtt                                                                     <  1:452359/72‑1 (MQ=255)

                                                                                                          ttATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAt  >  2:143463/1‑139 (MQ=255)

                                                                                                          ttATCTGGAATTCCTTATCCTGTTTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAt  >  1:126409/1‑139 (MQ=255)

CTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTT‑TT‑TGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAT  >  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