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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

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	89.3%	76.8 / 3.3	28	intergenic (+173/+329)	tyrB/yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
Reads supporting (aligned to +/- strand): ref base . (0/3); new base T (11/14); total (11/17)
Fisher's exact test for biased strand distribution p-value = 2.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

TTAAACTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑G‑TTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTA  >  NC_000913/4268348‑4268595

ttAAACTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑G‑tttttt                                                                                                               >  1:671803/1‑139 (MQ=255)

   aaCTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑G‑ttttttttg                                                                                                            >  1:361535/1‑137 (MQ=255)

      tGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑G‑TTTTTTTGGGTg                                                                                                         <  1:442929/139‑1 (MQ=255)

        tcgtcgCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTgg                                                                                                        >  2:224918/1‑139 (MQ=255)

        tcgtcgCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTgg                                                                                                        >  1:1084170/1‑139 (MQ=255)

                      atttctttATAGATGATTTTTTTGAGGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTGTTGTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑TAT‑TTTTTTTGGGTGGAGTAATAATTTCTg                                                                                          <  2:84631/138‑1 (MQ=255)

                             tataGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCt                                                                                   <  1:224918/139‑1 (MQ=255)

                                 gatgatTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAAcc                                                                               >  1:1099295/1‑139 (MQ=255)

                                                gCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaat                                                                >  1:1100532/1‑139 (MQ=255)

                                                   aTCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaataat                                                             <  2:34107/139‑1 (MQ=255)

                                                         cTACTTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAAATCCTTATCCTT‑T‑TTTTTTTTGGTGGAGTAATATTTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTAt                                                       <  2:686647/139‑1 (MQ=255)

                                                             gTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCggg                                                   <  2:593605/139‑1 (MQ=255)

                                                                  agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGt                                              <  1:874355/139‑1 (MQ=255)

                                                                  agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑G‑ttttttttggg                                                                                                          <  1:737555/78‑5 (MQ=255)

                                                                  agaTAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑G‑ttttttttggg                                                                                                          >  2:737555/1‑74 (MQ=255)

                                                                          aaCGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAg                                      <  1:130988/139‑1 (MQ=255)

                                                                            cGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCattatt                                                                         <  1:451375/102‑1 (MQ=255)

                                                                            cGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCattatt                                                                         >  2:451375/1‑102 (MQ=255)

                                                                               tgttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAAc                                                                                >  2:210046/1‑92 (MQ=255)

                                                                               tgttAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAAc                                                                                <  1:210046/92‑1 (MQ=255)

                                                                                          ttATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCt                      <  2:671803/139‑1 (MQ=255)

                                                                                                    gCTTATCCCAATTACCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCTCATCTAACCATTATTAAATTTAGTCATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATg            <  1:681785/139‑1 (MQ=255)

                                                                                                      ttATCCCAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCt          <  2:1100532/139‑1 (MQ=255)

                                                                                                          cccAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                          <  1:441081/55‑1 (MQ=255)

                                                                                                          cccAATTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                          >  2:441081/1‑55 (MQ=255)

                                                                                                              aTTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCggg                                                   >  1:663301/1‑90 (MQ=255)

                                                                                                              aTTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCggg                                                   <  2:663301/90‑1 (MQ=255)

                                                                                                              aTTATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTa  >  1:838175/1‑139 (MQ=255)

                                                                                                               ttATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAAc                                                                                <  2:420679/60‑1 (MQ=255)

                                                                                                               ttATCTGGAATTCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAAc                                                                                >  1:420679/1‑60 (MQ=255)

                                                                                                                         ttCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCtat                           <  1:932706/103‑1 (MQ=255)

                                                                                                                         ttCCTTATCC‑T‑GTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCtat                           >  2:932706/1‑103 (MQ=255)

TTAAACTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCC‑T‑G‑TTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTA  >  NC_000913/4268348‑4268595

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A