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 F68 I0 R1	25	50.4	1217238	93.3%	1135683	133.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,472	G→A	44.6%	A67V (GCT→GTT)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,472	0	G	A	44.6%	14.3 / 37.2	44	A67V (GCT→GTT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base G (8/15); new base A (9/10); total (19/25)
Fisher's exact test for biased strand distribution p-value = 5.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATT  >  USA300TCH1516_ALE/1744345‑1744597

tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAg                                                                                                                         <  1:167309/134‑1 (MQ=255)

 ttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTTCAAAGCCAATCCCCTTTGAATAAGCTACAgg                                                                                                                        >  1:121743/1‑134 (MQ=255)

   aaTTGTATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGAc                                                                                                                      <  1:483236/134‑1 (MQ=255)

   aaTTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGAc                                                                                                                      >  1:118769/1‑134 (MQ=255)

         aTCTTTGTGCATTGTTAAAACATTTGTACCCTCCTCAACGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCaa                                                                                                                <  1:110614/134‑1 (MQ=255)

          tCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATAACAATTGAATAAACTAACGGACAACCAAt                                                                                                               >  2:228362/1‑134 (MQ=255)

             ttGTGCATTGTTAAAACATTTGTATCATATTCTTGGTCATACTTATAACTAATGACTTCACGAGGTAATAACCCTGCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGAt                                                                                                            <  1:202506/134‑1 (MQ=255)

             ttGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCaccgac                                                                                                            >  2:285241/1‑129 (MQ=255)

                    ttGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCa                                                                                                     <  1:88631/134‑1 (MQ=255)

                     tGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGCATAAACTACAGGACAGCCACTGATAAAGCCAc                                                                                                    >  1:519126/1‑134 (MQ=255)

                       ttAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATACACTCAcgc                                                                                                  >  1:16976/1‑134 (MQ=255)

                         aaaaCATTTGTAACATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCAAgcgc                                                                                                >  2:58607/1‑134 (MQ=255)

                               tttGTACCATATTCTAGGTCATATTCTTAACGAATGTCTTCACTAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAgg                                                                                          <  1:343511/134‑1 (MQ=255)

                                        tatTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAAc                                                                                 <  2:118769/134‑1 (MQ=255)

                                               ggTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAAGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCa                                                                          >  1:350876/1‑134 (MQ=255)

                                               ggTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTCAATAATCTACATGACAGCCCATAATCAACCCACGCACTTCAGTTCCTACAACGATATCa                                                                          >  1:130876/1‑134 (MQ=255)

                                                   aTACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGCTAAAGCCACGCTCTTCAGGTCCTACAACGTTCTCAAcct                                                                      >  1:27901/1‑132 (MQ=255)

                                                     aCTCATATCGAATGACTTCACGTAGTAATTCCCCTTCTTTCCTAACAGGCGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACAtct                                                                    <  1:579356/134‑1 (MQ=255)

                                                        cttAACTAATGACTTCACGTGGTAATTTTCCTTCTTTTCTAACAGGTGCAAAGCCAATCTCCATTGAATAAGCTACAGTACAGCCAATGATAGAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                                                 <  2:292280/132‑1 (MQ=255)

                                                         atcgcGAATGACTTCACGAGGTCATTTCCCTTCTTTGCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAAGACGTCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGt                                                                <  2:602686/130‑1 (MQ=255)

                                                         aTAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCCTTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGAAATCAACATCTCTGt                                                                >  2:346726/1‑134 (MQ=255)

                                                         aTAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAAGTCAAACAACGATATCAATATATTTGt                                                                >  1:77780/1‑134 (MQ=255)

                                                         aTAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAACGATAAAGCCACGCGCTACAGGTCCTACAACGAAATCAACAtctcaca                                                                >  1:32544/1‑131 (MQ=255)

                                                                aTGACTCCACGAGGTCATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGc                                                         <  2:520253/134‑1 (MQ=255)

                                                                       cACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCt                                                  <  2:532655/134‑1 (MQ=255)

                                                                       cACGAGGTAATGTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCTTAACACAATTGCAACATCTCTGTCTTTTGCGTATTCt                                                  <  2:131209/134‑1 (MQ=255)

                                                                                   tctctttttTTCTAACAAGTGCAAAGCCAATCCCAATTGAATAAACCACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCt                                      <  1:20735/131‑1 (MQ=255)

                                                                                   tCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCATCATCTCTGTCTTTTGCGTATTCTACAATTTTATCt                                      >  1:337237/1‑134 (MQ=255)

                                                                                   tCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCt                                      <  1:210342/134‑1 (MQ=255)

                                                                                       ttcttTTCTAACCGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTg                                  <  1:362788/134‑1 (MQ=255)

                                                                                       ttcttTTCTAACAGGTGCAAAGCCAATAACTTCTTAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTg                                  <  2:268017/134‑1 (MQ=255)

                                                                                          ttttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAATGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCAt                               <  1:455920/134‑1 (MQ=255)

                                                                                                agcatgTGCAAATCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCat                         <  2:447191/129‑1 (MQ=255)

                                                                                                aaCAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCat                         <  1:426607/134‑1 (MQ=255)

                                                                                                aaCAGATGCAAAGCCAATCGCCATTTAATGATCGACAGGACAGCCAATGATAAAGCCACGCGCTTGAGGTCCTACACCGATATCAACATCTCTGTCTTTTGCGTCTTCTACAATTCTATCTGTTGCACGGCCat                         >  1:143995/1‑134 (MQ=255)

                                                                                                   aGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATg                      >  1:337418/1‑134 (MQ=255)

                                                                                                    ggTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTATCGTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGc                     >  2:150142/1‑134 (MQ=255)

                                                                                                          aaGCCCAGCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCAcc               <  2:519126/134‑1 (MQ=255)

                                                                                                                  ctccATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCa       <  1:61946/132‑1 (MQ=255)

                                                                                                                  ccccATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCa       <  1:484801/134‑1 (MQ=255)

                                                                                                                  ccccATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTATATCTGTTGCATAGCCATATGATTCACAATTATCCa       >  2:403493/1‑134 (MQ=255)

                                                                                                                   cccATTGAATAAGCTACAAGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCAt      <  2:350876/134‑1 (MQ=255)

                                                                                                                    ccATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATa     <  1:332847/134‑1 (MQ=255)

                                                                                                                       ttGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCACCCTCTCTGTCTTTTGCGTATTCTACACTTTTGTCTGTTGCATAGCCATATCCTCTGCCAATCTCCattatt  >  1:192260/1‑134 (MQ=255)

TTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATT  >  USA300TCH1516_ALE/1744345‑1744597

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