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	2,719,269:1	(A)_5→6	100%	coding (213/705 nt)	USA300HOU_2573 →	dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,719,264	1	.	A	52.8%	64.3 / 67.1	36	coding (208/705 nt)	USA300HOU_2573	dehydrogenase
Reads supporting (aligned to +/- strand): ref base . (8/9); new base A (11/8); total (19/17)
Fisher's exact test for biased strand distribution p-value = 7.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

GCATTGGGTTACAAAGTTTATATAGGTTCTCGGAATGATGTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGTATATCAAACGAATGTATTCGGTATCGTACGAATGA  >  CP000730/2719126‑2719396

gCATTGGGTTACAAAGTTTATATAGGTTCTCGGAATGATGTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑aa                                                                                                                                     >  1:270498/1‑141 (MQ=255)

   ttGGGTTACAAAGTTTATATAGGTTCTCGGAATGATGTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑aa‑aaa                                                                                                                                 >  2:219962/1‑141 (MQ=255)

        ttACAAAGTTTATATAGGTTCTCGGAATGATGTAAGAGCACAACAAGCAACAACGAAATAAGGTCCGCTATAAGCACTGTTAGATATAATAGGTTATGTCTCGATCAATAATGTTTATAACATAATTGCTG‑ca‑aaaacaag                                                                                                                            >  2:205060/1‑136 (MQ=255)

                  tatataGGTTCTCGGAATGATGTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGa                                                                                                                   <  1:218156/141‑1 (MQ=255)

                    tataGGTTCTCGGAATGATGTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGata                                                                                                                 <  2:176326/141‑1 (MQ=255)

                      taGGTTCTCGGAATGATGTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATcc                                                                                                              <  2:21705/141‑1 (MQ=255)

                               ggAATGATGTAAGAGGACAACCAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTAAAAGTGACTACTCAGTCAAAAATCCTTATAAACTGATTGATG‑AA‑AACGAAACCCGACTTGATATCCTcgtgagca                                                                                                     >  2:192544/1‑134 (MQ=255)

                               ggAATGATGTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAAc                                                                                                      >  1:16744/1‑141 (MQ=255)

                                  atgatgTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATg                                                                                                  >  1:177070/1‑141 (MQ=255)

                                   tgatgTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATg                                                                                                  >  2:143661/1‑141 (MQ=255)

                                   tgatgTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATg                                                                                                  >  2:143692/1‑141 (MQ=255)

                                    gatgTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGc                                                                                                 <  1:193232/141‑1 (MQ=255)

                                                   aaaaaataaaaaaaaTTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCaa                                                                                 <  2:83453/131‑1 (MQ=255)

                                                               aaaTTAGGTGTTCATTATGTACAATTAGATGTTATAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCt                                                                     <  2:119656/141‑1 (MQ=255)

                                                                    aGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCa                                                                 >  1:216230/1‑141 (MQ=255)

                                                                     ggTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCaaa                                                               >  1:76143/1‑141 (MQ=255)

                                                                      gtgtTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAAt                                                              <  2:108389/141‑1 (MQ=255)

                                                                        tttCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTg                                                            <  2:217652/140‑1 (MQ=255)

                                                                                tGTACAATTAGATGTGACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCg                                                    <  2:177070/141‑1 (MQ=255)

                                                                                 gTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGt                                                   >  2:260337/1‑141 (MQ=255)

                                                                                  tACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGTAGGTATATCTGGTCAATTTTCAGCACCTCCCAAATTGACACCTCGTg                                                  >  2:38385/1‑141 (MQ=255)

                                                                                  tACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGCATATCTGGTCAATTTTCAGCACCTTCCAAATTGGCACCTCGTg                                                  >  1:136731/1‑141 (MQ=255)

                                                                                       tgaGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGTCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCAGCTTCCAAATTGACACCTCGTGACGt                                              <  2:270157/139‑1 (MQ=255)

                                                                                         aGATGTTACAAGTGACTACGCAGTCGAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTAGATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTg                                            <  2:94550/141‑1 (MQ=255)

                                                                                          aaTGTCACAAGTGACTACTCAGTCAAAAATGCTTATAACATTATTGCCG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTgaa                                          <  2:11217/140‑1 (MQ=255)

                                                                                           aTGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCCATTTTCAGCACCTTCCAAATTGACACCTCGTGCCGTTgaa                                          >  1:194020/1‑141 (MQ=255)

                                                                                               tACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGaagaag                                      <  2:227110/141‑1 (MQ=255)

                                                                                               tACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGaagaag                                      <  1:46412/141‑1 (MQ=255)

                                                                                                aCAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGt                                     >  1:276148/1‑141 (MQ=255)

                                                                                                 cAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCCGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGtat                                   <  1:276253/141‑1 (MQ=255)

                                                                                                   aGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGtata                                  >  1:58661/1‑141 (MQ=255)

                                                                                                   aGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATACTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCCAATTGACACCTCGTGACGTTGAAGAAGtata                                  >  2:51724/1‑141 (MQ=255)

                                                                                                       actactCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGTATAACaaa                             >  1:3577/1‑141 (MQ=255)

                                                                                                           ctCAGTCAAAAATGCTCATAAGATGATTGCTG‑AAGAAAGAATGGTGTCGTGATATCCTCTTTAACTATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGTATATCAAACGa                          <  2:110723/141‑1 (MQ=255)

                                                                                                              aGTCAAAAATGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACATCGTTACGTTGAAGAAGTATATCAAACGAATg                       <  2:116125/141‑1 (MQ=255)

                                                                                                                     aaTGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCAAATTCCTATTTGACACCTCGTGACGTTGAAGAAGTATATCAAACGAATGTATTCGGt               >  1:190789/1‑141 (MQ=255)

                                                                                                                       tGCTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGTATATCAAACGAATGTATTCGGTa              >  1:137366/1‑141 (MQ=255)

                                                                                                                         cTTATAACATGATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGTATATCAAACGAATGTATTCGGTATc            >  1:244268/1‑141 (MQ=255)

                                                                                                                                   gATTGCTGAAA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGTATATCAAACGAATGTATTCGGTATCGTACGAatga  >  1:168547/1‑141 (MQ=255)

GCATTGGGTTACAAAGTTTATATAGGTTCTCGGAATGATGTAAGAGGACAACAAGCATCACAAAAATTAGGTGTTCATTATGTACAATTAGATGTTACAAGTGACTACTCAGTCAAAAATGCTTATAACATGATTGCTG‑AA‑AAAGAAGGCCGTCTTGATATCCTCATTAACAATGCAGGTATATCTGGTCAATTTTCAGCACCTTCCAAATTGACACCTCGTGACGTTGAAGAAGTATATCAAACGAATGTATTCGGTATCGTACGAATGA  >  CP000730/2719126‑2719396

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