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
A1 F169 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,830,883	C→T	75.3%	K79K (AAG→AAA)	ezrA ←	Septation ring formation regulator EzrA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,830,883	0	C	T	75.3%	43.8 / 10.4	28	K79K (AAG→AAA)	ezrA	Septation ring formation regulator EzrA
Reads supporting (aligned to +/- strand): ref base C (4/3); new base T (10/11); total (14/14)
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

AGCTTTGTTCGTAACTATCCATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATACTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCAAAAGGTAACGTCTCAATTTCATTTTTACGTTCGAT  >  USA300TCH1516_ALE/1830759‑1831017

aGCTTTGTTCGTAACTGTCCATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATACTTATTTGTACTTTCTa                                                                                                                        >  1:234804/1‑141 (MQ=255)

 gCTTTGTTCGTAACTATCCATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTCTCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCCCAGGAGCTAGATATTTATTTGTACTTTCtcc                                                                                                                       >  2:118534/1‑139 (MQ=255)

   tttGTTCGTAACTATCCATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATACTTATTTGTACTTTCTACGt                                                                                                                     >  2:274986/1‑141 (MQ=255)

     tGTTCGTAACTATACATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTg                                                                                                                   <  1:324198/141‑1 (MQ=255)

         cGTAACTATCCATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCt                                                                                                               >  1:18274/1‑141 (MQ=255)

            aaCTATCCATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCtttt                                                                                                            >  1:135463/1‑141 (MQ=255)

               tATCCATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTGATGTGGACTTTCTACGTTGTCCTTTTTCa                                                                                                         <  1:191391/141‑1 (MQ=255)

                         ccgcttttCATCATCAATTTCACATTCAGATGCGTTGAAACTAAAGTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGCTGCTAGATACTTATTTGTACCTTCTACGTTGTCCTTTTTCATTGCATCGTa                                                                                               <  2:29543/137‑1 (MQ=255)

                            aTTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATACTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTAttt                                                                                            >  1:333305/1‑141 (MQ=255)

                                gCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGtt                                                                                        >  2:23443/1‑141 (MQ=255)

                                         aTTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATTAAGCTTCAGCATTATGTATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCa                                                                               <  2:65901/141‑1 (MQ=255)

                                               cTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTACTGTTCCAAAGGAGGTAGAGATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCtttt                                                                         >  1:189776/1‑141 (MQ=255)

                                                tttttgaTGCTTTGAATCTAAATTTATTTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTa                                                                        <  1:113731/136‑1 (MQ=255)

                                                tttGAGATGCGTTGAAACTAAACTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATACTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTa                                                                        <  1:43913/141‑1 (MQ=255)

                                                           ttGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTGCACAGGAGCTAGATCTTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTTTCCTTTGAAGTTCAACTTa                                                             >  1:272638/1‑141 (MQ=255)

                                                             gAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGa                                                           <  1:180167/141‑1 (MQ=255)

                                                             gAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGa                                                           <  1:116661/141‑1 (MQ=255)

                                                                       ttATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCa                                                 <  2:307426/141‑1 (MQ=255)

                                                                              ataaAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGtttt                                          >  2:123196/1‑141 (MQ=255)

                                                                                  aGCCTCAGTATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATc                                      <  1:23443/141‑1 (MQ=255)

                                                                                     cTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCaaa                                   >  1:360174/1‑141 (MQ=255)

                                                                                      tCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATACTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCaaaa                                  >  2:56411/1‑141 (MQ=255)

                                                                                       cAGCATTATTGATTTTTTCGGCCACAGGAGCTAGATACTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCAAAAg                                 <  1:130302/141‑1 (MQ=255)

                                                                                          cATTATGGATTTTTTCTTCCACAGGAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCAAAAGGTa                              >  1:256056/1‑141 (MQ=255)

                                                                                                                  gAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCAAAAGGTAACGTCTCAATTTCATTTTTACGtt      <  1:92144/141‑1 (MQ=255)

                                                                                                                  gAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCAAAAGGTAACGTCTCAATTTCATTTTTACGtt      <  1:351326/141‑1 (MQ=255)

                                                                                                                  gAGCTAGATATTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCAAAAGGTAACGTCTCAATTTCATTTTTACGtt      <  1:341104/141‑1 (MQ=255)

                                                                                                                      tAGATATTTATTTGTACTTTCTCCTTTGGCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCAAAAGGTAACGTCTCAATTTCATTTTTACGTTCGAt  >  1:291154/1‑141 (MQ=255)

AGCTTTGTTCGTAACTATCCATCAACTCATTTGCATCATCAATTTCACTTTGAGATGCGTTGAAACTAAATTTATCTAATAAAGCCTCAGCATTATGGATTTTTTCTTCCACAGGAGCTAGATACTTATTTGTACTTTCTACGTTGTCCTTTTTCATTGCATCGTATTTCGTTTTTGTTTCACCTTTTAAATTCAACTTAGATAATTGTGCAAGGTTTTGATCAAAAGGTAACGTCTCAATTTCATTTTTACGTTCGAT  >  USA300TCH1516_ALE/1830759‑1831017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A