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
A13 F191 I1 R2	32	34.5	741600	95.9%	711194	140.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,386,119	G→A	P114L (CCG→CTG)	USA300HOU_2245 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,386,119	0	G	A	90.0%	82.5 / ‑0.0	30	P114L (CCG→CTG)	USA300HOU_2245	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (1/2); new base A (18/9); total (19/11)
Fisher's exact test for biased strand distribution p-value = 5.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCCGCCTT  >  CP000730/2385986‑2386254

aGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCctac                                                                                                                                  <  2:8555/141‑1 (MQ=255)

   aCGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCtactac                                                                                                                               >  2:323908/1‑141 (MQ=255)

     gCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACtt                                                                                                                             <  1:118854/141‑1 (MQ=255)

     ccATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGCTTATCTCTTTCCATTTGAATCAGCCCTACTACtt                                                                                                                             <  2:127370/140‑1 (MQ=255)

            aTCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTg                                                                                                                      <  2:255813/141‑1 (MQ=255)

              cACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGcc                                                                                                                    >  2:321995/1‑140 (MQ=255)

              cACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCt                                                                                                                    <  2:225453/141‑1 (MQ=255)

                      tcCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGt                                                                                                            >  2:109665/1‑141 (MQ=255)

                                tAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                                  >  2:191494/1‑141 (MQ=255)

                                  aaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTa                                                                                                >  1:197244/1‑141 (MQ=255)

                                     aaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACt                                                                                             <  1:184631/141‑1 (MQ=255)

                                         gtggCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCct                                                                                         >  1:132085/1‑141 (MQ=255)

                                         gtggCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCct                                                                                         >  1:132032/1‑141 (MQ=255)

                                                     catcatcatCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCAtttt                                                                             >  2:180373/1‑140 (MQ=255)

                                                       tcatcatcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTa                                                                           <  1:35095/141‑1 (MQ=255)

                                                       tcatcatcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTa                                                                           >  1:273966/1‑141 (MQ=255)

                                                                      aTTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTGCTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttt                                                            <  2:208330/141‑1 (MQ=255)

                                                                                gCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCtt                                                  >  1:216123/1‑141 (MQ=255)

                                                                                gCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCtt                                                  >  1:127654/1‑141 (MQ=255)

                                                                                      gCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                            <  1:142603/141‑1 (MQ=255)

                                                                                      gCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                            <  1:8565/141‑1 (MQ=255)

                                                                                      gCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                            <  1:23886/141‑1 (MQ=255)

                                                                                      gCCACTTTACCTTACCATCTGTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCGACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                            >  2:62920/1‑141 (MQ=255)

                                                                                        cACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATAc                                          >  2:155175/1‑141 (MQ=255)

                                                                                             taccttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTtctc                                     >  1:336622/1‑141 (MQ=255)

                                                                                                cttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTg                                  >  1:200423/1‑141 (MQ=255)

                                                                                                 ttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGa                                 >  1:101845/1‑141 (MQ=255)

                                                                                                  taccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTATTAATGGTCTCTTGAGCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGaa                                >  1:312587/1‑141 (MQ=255)

                                                                                                             tgtgTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTa                     >  2:81769/1‑141 (MQ=255)

                                                                                                                                gAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCCGCCtt  >  1:345555/1‑141 (MQ=255)

AGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCCGCCTT  >  CP000730/2385986‑2386254

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

GATK/CNVnator alignment

N/A