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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

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	89.7%	80.5 / 4.1	29	intergenic (+173/+329)	tyrB/yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
Reads supporting (aligned to +/- strand): ref base . (1/2); new base T (9/17); total (10/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.51e-01

AAATTAAACTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAT  >  NC_000913/4268345‑4268596

aaaTTAAACTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑ttt                                                                                                                   >  2:700734/1‑139 (MQ=255)

        cTGTCGTCGCTTTTACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTtggg                                                                                                           <  1:372987/139‑2 (MQ=255)

        cTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑ttttttttggg                                                                                                           <  1:78468/139‑5 (MQ=255)

          gtcgtcGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTg                                                                                                          <  1:587099/139‑1 (MQ=255)

                    tCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTaataat                                                                                                <  1:198877/139‑1 (MQ=255)

                         ctttctttATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:668629/139‑1 (MQ=255)

                         ctttctttATAGATGATTTTTTTGAAGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:513270/139‑1 (MQ=255)

                            tctttATAGATGATTTTATTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTtggg                                                                                                           >  2:83437/1‑118 (MQ=255)

                            tctttATAGATGATTTTATTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTtggg                                                                                                           <  1:83437/119‑2 (MQ=255)

                                 ataGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTa                                                                                   >  1:255059/1‑139 (MQ=255)

                                    gatgatTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           >  1:531533/1‑128 (MQ=255)

                                    gatgatTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  2:531533/128‑1 (MQ=255)

                                               tGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAAtt                                                                     <  1:311116/139‑1 (MQ=255)

                                                 aTGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACAt                                                                                      <  1:734904/120‑1 (MQ=255)

                                                 aTGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACAt                                                                                      >  2:734904/1‑120 (MQ=255)

                                                     cATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaataa                                                               <  1:700734/139‑1 (MQ=255)

                                                      aTCGTTCTACGTGAGAGATAATATACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTtaataat                                                              <  2:17609/139‑1 (MQ=255)

                                                                 tGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATCCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGt                                                   <  1:719246/139‑1 (MQ=255)

                                                                       ataataAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTAt                                                        >  1:334870/1‑128 (MQ=255)

                                                                       ataataAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTAt                                                        <  2:334870/128‑1 (MQ=255)

                                                                          ataaACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCgg                                                     >  2:878271/1‑128 (MQ=255)

                                                                          ataaACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCgg                                                     <  1:878271/128‑1 (MQ=255)

                                                                           taaACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGAt                                         >  1:832601/1‑139 (MQ=255)

                                                                                                   ttAAGCTTATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGaa                 <  2:255059/139‑1 (MQ=255)

                                                                                                         ttATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCt           <  2:649978/139‑1 (MQ=255)

                                                                                                         ttATCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCt           <  1:881251/139‑1 (MQ=255)

                                                                                                           aTCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           >  2:186246/1‑57 (MQ=255)

                                                                                                           aTCCCAATTATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTg                                                                                           <  1:186246/57‑1 (MQ=255)

                                                                                                                  ttATCTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAt  >  2:582653/1‑139 (MQ=255)

                                                                                                                      cTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGca                                                                                         >  2:813749/1‑48 (MQ=38)

                                                                                                                      cTGGAATTCCTTATCCTGTTTTTTTTGGGTGGAGTAATAATTTCTGca                                                                                         <  1:813749/48‑1 (MQ=38)

AAATTAAACTGTCGTCGCTTTCACTCTTTCTTTATAGATGATTTTTTTGATGCCATCGTTCTACGTGAGAGATAATAAACGTTGTTAGTTCTTTTATTGTTAAGCTTATCCCAATTATCTGGAATTCCTTATCCTG‑TTTTTTTGGGTGGAGTAATAATTTCTGCACATCTAACCATTATTAAATTTAATAATAAGTATCGGGTTTGTTACGATAGAATATTTCTATATCCTCAAGAATATGCTTTGCCTTAT  >  NC_000913/4268345‑4268596

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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