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
A15 F116 I0 R1	44	26.4	562224	96.5%	542546	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,027,561	G→C	49.8%	T129S (ACC→AGC)	vraS ←	sensor histidine kinase VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,027,561	0	G	C	49.8%	‑0.9 / 22.1	22	T129S (ACC→AGC)	vraS	sensor histidine kinase VraS
Reads supporting (aligned to +/- strand): ref base G (7/4); new base C (6/5); total (13/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTT  >  CP000730/2027426‑2027680

ttGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTaat                                                                                                                    >  2:201586/1‑140 (MQ=255)

ttGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAg                                                                                                                    >  2:201491/1‑141 (MQ=255)

    tagcagatagcaTCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGGAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTCAGtttt                                                                                                                >  1:61908/1‑141 (MQ=255)

        agatagcaTCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGt                                                                                                            >  2:75192/1‑141 (MQ=255)

            agcaTCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTa                                                                                                        <  1:45541/141‑1 (MQ=255)

                     cTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAAc                                                                                               >  1:44886/1‑141 (MQ=255)

                            aaaaaaGTTGCTGACTAACAGAATCGAAAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCa                                                                                        <  2:126419/140‑1 (MQ=255)

                                 aGTTGCTGACTAACAGAATCATGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCt                                                                                   <  2:138059/141‑1 (MQ=255)

                                 aGTTGCTGACTAACAGAATCATGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTCAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCt                                                                                   <  2:137968/141‑1 (MQ=255)

                                           tAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACAACATTAATATTATAATTTTCATTGCTTAAGTTTTCAGTTTTAAGTCGCAACTTATGGAATTCTTGATTTAAAg                                                                         <  1:156213/141‑1 (MQ=255)

                                                         aGTTCTCGTGCTAGTCTTTCACGTTCATCTTCAATAATATTTTTAACTTTCACAGCATTAATATTATAATTTTGATTTCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATgg                                                           >  2:82064/1‑141 (MQ=255)

                                                            tctcGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTAAAAGTGTATGGtat                                                        >  2:163125/1‑141 (MQ=255)

                                                             ctcGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGtata                                                       <  1:153682/141‑1 (MQ=255)

                                                               cGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATaaa                                                     >  1:114737/1‑141 (MQ=255)

                                                                   ctcgTCTTTGACGTTCATCATCAATAATCTTTTTAACTTTCCCATCATTAATATTATCATTTTCATTGGTTAAGTTTTGAGTTTTAAATCGCAACTTATGCAATTCTTGAGTTAAAGATACAAGTGTATGGTATACAtgtc                                                 >  2:144500/4‑138 (MQ=255)

                                                                    tAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTaa                                                <  1:47305/141‑1 (MQ=255)

                                                                     aGTTTTTGACTTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAAc                                               <  2:242008/141‑1 (MQ=255)

                                                                      gTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGCTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACg                                              <  1:185317/141‑1 (MQ=255)

                                                                                         aataatCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCtat                           >  1:44781/1‑141 (MQ=255)

                                                                                                 ttttAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGAt                   >  1:26711/1‑141 (MQ=255)

                                                                                                          tCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGc          >  1:15681/1‑141 (MQ=255)

                                                                                                                  ttAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGtt  >  2:147641/1‑141 (MQ=255)

TTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTT  >  CP000730/2027426‑2027680

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A