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
A19 F166 I0 R1	50	63.8	1389156	94.9%	1318309	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,232,148	G→T	100%	G18V (GGC→GTC)	USA300HOU_1157 →	non‑specific serine/threonine protein kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,232,148	0	G	T	98.1%	105.5 / ‑5.8	39	G18V (GGC→GTC)	USA300HOU_1157	non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand): ref base G (1/0); new base T (21/16); total (22/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTGATCAATTAATGCAATTGGCATTAGATAACCATTCGAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAACGTTTT‑GAACGAGAAGTACATAACTCATCA  >  CP000730/1232011‑1232284

gTGATCAATTAATGCAATTGGCATTAGATAACCATTCGAGAGATAGCGTTCCTGTCATATACGATACGAGTGAAGGTGATAAAGTATGATATGTTCAATAATAAATGAAGGATATGAAATTGTAGATAAGCTTGGcgtcgg                                                                                                                                        >  2:335756/1‑141 (MQ=255)

gTGATCAATTAATGCAATTGGCATTAGATAACCATTCGAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGcgtcgg                                                                                                                                        >  2:165311/1‑141 (MQ=255)

   aTCAATTAATGCAATTGGCATTAGATAACCATTCGAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTgg                                                                                                                                     >  1:545627/1‑141 (MQ=255)

        ttAATGCAATTGGCATTAGATAACCATTCGAAAGATAACGTTACTTACATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCCTGGCGTCGGTGGCATGa                                                                                                                                >  2:33241/1‑141 (MQ=255)

        ttAATGCAATTGGCATTAGATAAAAAGTCTAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGAATGa                                                                                                                                >  2:149494/1‑141 (MQ=255)

                aTTGGCATTAGATAACCATTCGAAAGATAACGCTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCAGGAGTAACGtt                                                                                                                        >  1:199591/1‑141 (MQ=255)

                aTTGGCATGAGATAACCATTCGAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGtt                                                                                                                        >  1:443965/1‑141 (MQ=255)

                    gCATTAGATAACCATTCGAAAGATAACGTTACTTTGATACTCGCGGCTATTGAAGGTGATGAAGTATGATAGGTTAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGGGTGGGTGGCATGGGTACCGTTTAtt                                                                                                                    >  2:421505/1‑140 (MQ=255)

                       ttAGATAACCATTCGAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTg                                                                                                                 >  2:438500/1‑141 (MQ=255)

                                 aTTCGAAAGAAAACGATACTTTCATACTCGCGGCTATTGAAGGTGAAGTCGGATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAgatac                                                                                                       <  1:226247/141‑1 (MQ=255)

                                  ttCGAAAGATAACGTTTCTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAgatacg                                                                                                      <  2:332760/141‑1 (MQ=255)

                                   tCGAAAAATAACGTTACTTTCATACTCGCGGCTATTGAAGTTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAgatacga                                                                                                     <  2:334694/141‑1 (MQ=255)

                                       aaGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACt                                                                                                 >  2:441216/1‑141 (MQ=255)

                                             aCGTTACTTTAAGACTCGCAGGTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACAt                                                                                           <  2:112313/141‑1 (MQ=255)

                                               gTTACTTTCATTTTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATTATAAATGAACGTTATAAAATTGTAGATAAGCTTGGCGCCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTa                                                                                         <  2:594330/141‑1 (MQ=255)

                                               gTTACTTTCATACTCGCGGCTATTGAAGGTGATTAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAAGATTa                                                                                         <  1:473095/141‑1 (MQ=255)

                                               gTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAACTCCTGGATTAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATCCTTAACATTa                                                                                         <  1:504316/141‑1 (MQ=255)

                                                     ttCATACTGGCGGCTATTGAAGGTGATAAAGTATGATCGGTAAAATCATAAATGAGCGATAAAAGAATGTAGATAAGCTTGGCGTCGGGGGCATGAGTAACGTTTAACTTGCTGAAGCTACGCTACTTAAGATTAAAGATg                                                                                   >  2:575660/1‑141 (MQ=255)

                                                     ttCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTg                                                                                   >  2:116662/1‑141 (MQ=255)

                                                             cgcgGCTATTGAAGGTGATAAAGTATCATAGGTAAAATAATAAATGAACGATAAAAAATTGTAGATAAGCTTGGGGTCGGAGGAATGAGTACCGTTTATCTTGCTAAAGATACGAGACTTACCATTAATGCTACAATTaat                                                                           >  2:431990/1‑140 (MQ=255)

                                                               cgGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGGTGCAATTAAGGc                                                                         >  1:555270/1‑141 (MQ=255)

                                                                     ttGAAGGTGATAAAGTATGATCGTTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGAtttt                                                                   <  1:312219/141‑1 (MQ=255)

                                                                     ttGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGCACGATATACAATTGACACTATACATGGGGGCTTGGTTGTTATTATTGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGGGAtttt                                                                   >  1:137878/1‑141 (MQ=255)

                                                                     ttGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGAtttt                                                                   <  1:126219/141‑1 (MQ=255)

                                                                     ttGAAAGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGAtttt                                                                   <  1:555051/141‑1 (MQ=255)

                                                                       aaaaaacaTAAAGACTGATAGGTAAAATAATAAATTAATGAAACAAAATTGCAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTta                                                                 <  2:32923/134‑1 (MQ=255)

                                                                           gTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCTGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATacc                                                             >  2:179677/1‑141 (MQ=255)

                                                                               tAAAGTATGATAAGTAAAAGAATAAATGAAAGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCt                                                         <  2:691545/141‑1 (MQ=255)

                                                                                aaaGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTa                                                        >  1:430270/1‑141 (MQ=255)

                                                                                aaaGTATGATAGGTAAAATAATAAAGGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTa                                                        <  2:82904/141‑1 (MQ=255)

                                                                                   gTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTagag                                                     <  1:441216/141‑1 (MQ=255)

                                                                                         tatgtcacataataAATGTCCGAATTAAAATTGGAGATAAGCTGGGCGTCGGTGGCATGAGTACAGTGTAGCTTGCTGCAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAaag                                               <  1:161436/133‑1 (MQ=255)

                                                                                          aGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATCAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAaaga                                              <  1:368057/141‑1 (MQ=255)

                                                                                                aataatAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGaaaa                                        >  2:160289/1‑140 (MQ=255)

                                                                                                aataatAAATGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAAAAGAAAc                                        >  2:277572/1‑141 (MQ=255)

                                                                                                        aTGAACGATATAAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAAc                                >  1:673885/1‑141 (MQ=255)

                                                                                                                  taAAATTGTAGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCCATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAAGGTTTA‑GAACg                     >  2:172465/1‑141 (MQ=255)

                                                                                                                           aGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAACGTTTT‑TAACGAGAAGTACa            >  2:97415/1‑141 (MQ=255)

                                                                                                                           aGATAAGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAACGTTTT‑GAACGAGAAGTACa            <  1:152051/141‑1 (MQ=255)

                                                                                                                                aGCTTGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAACGTTTT‑GAACGAGAAGTACATAACt       >  1:99365/1‑141 (MQ=255)

                                                                                                                                   ttGGCGTCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAACGTTTT‑GAACGAGAAGTACATAACtcat    >  1:666407/1‑141 (MQ=255)

                                                                                                                                     ggcgtcGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAACGTTTTAGAACG‑GAAGTACATAACtcataa  >  2:105890/1‑139 (MQ=255)

GTGATCAATTAATGCAATTGGCATTAGATAACCATTCGAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTAAAGTTGCAATTAAGGCGATTTTTATACCACCTAGAGAAAAAGAAGAAACATTAAAACGTTTT‑GAACGAGAAGTACATAACTCATCA  >  CP000730/1232011‑1232284

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A