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 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,358,236	A→G	G300G (GGA→GGG)	hom →	Homoserine dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,358,236	0	A	G	97.8%	167.0 / ‑2.1	45	coding (900/1281 nt)	hom	Homoserine dehydrogenase
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (22/22); minor base . (1/0); total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.43e-01

GAATATATGAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGAGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAGATAAAACACGGGAAATGATGGATTCAG  >  USA300TCH1516_ALE/1358091‑1358372

gAATATATGAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGgc                                                                                                                                        >  4:42856/1‑148 (MQ=255)

 aaTATATGAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGgca                                                                                                                                       >  3:324966/1‑148 (MQ=255)

      atGAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGgcaggcag                                                                                                                                  <  3:325762/148‑1 (MQ=255)

      atGAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGgcaggcag                                                                                                                                  <  3:96315/148‑1 (MQ=255)

      atGAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGgcaggcag                                                                                                                                  <  4:295994/148‑1 (MQ=255)

      atGAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGgcaggcag                                                                                                                                  <  4:406396/148‑1 (MQ=255)

        gAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGtt                                                                                                                                <  3:330505/148‑1 (MQ=255)

         aaaaTGGCAAAGTTAATTCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGttt                                                                                                                               >  3:381785/1‑148 (MQ=255)

         aaaaTGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGttt                                                                                                                               >  3:205607/1‑148 (MQ=255)

         aaaaTGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGttt                                                                                                                               >  3:412189/1‑148 (MQ=255)

            atcgccaaGTTAACGCATCGGCAGAACCAACTTTAATCGATAAACAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGggcaggca                                                                                                                                   <  1:4999/135‑1 (MQ=255)

                      tAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGt                                                                                                                  >  4:237340/1‑148 (MQ=255)

                          gCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCg                                                                                                              <  3:54882/148‑1 (MQ=255)

                              cGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGt                                                                                                          <  3:112301/148‑1 (MQ=255)

                                   gAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTg                                                                                                     >  4:171053/1‑148 (MQ=255)

                                     aCCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGAt                                                                                                   <  3:25058/148‑1 (MQ=255)

                                     aCCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGAt                                                                                                   <  3:367674/148‑1 (MQ=255)

                                             tAATTGATAAAAAGCATCAATTAGGAGGTGTAGAGGATGAATATAACGCGATTTCTGTTATTGGTGATGCCGTTGGTGACACGCTGTTTTATGGAAAGGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATATATTGaa                                                                                           >  4:374242/1‑148 (MQ=255)

                                                ttGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTAt                                                                                               <  1:60059/141‑1 (MQ=255)

                                                  gATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAg                                                                                      >  3:377129/1‑148 (MQ=255)

                                                  gATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAg                                                                                      >  3:201081/1‑148 (MQ=255)

                                                          gCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTAGGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTc                                                                              <  4:270107/148‑1 (MQ=255)

                                                                 ttAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAAt                                                                       <  4:296315/148‑1 (MQ=255)

                                                                 ttAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAAt                                                                       >  3:233272/1‑148 (MQ=255)

                                                                        cTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGAttt                                                                >  3:10254/1‑148 (MQ=255)

                                                                         tGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTa                                                               <  3:76538/148‑1 (MQ=255)

                                                                         tGTAGAGGATGAATATAACGCCATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTAGGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATc                                                                      <  2:36365/141‑1 (MQ=255)

                                                                                   gAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGc                                                     >  4:271328/1‑148 (MQ=255)

                                                                                      tataACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGccac                                                  <  4:381785/148‑1 (MQ=255)

                                                                                      tataACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGccac                                                  <  4:412189/148‑1 (MQ=255)

                                                                                      tataACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGccac                                                  <  4:205607/148‑1 (MQ=255)

                                                                                        taACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGccacca                                                >  3:322453/1‑148 (MQ=255)

                                                                                          aCGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAGGG‑GCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACAt                                             >  4:354525/1‑148 (MQ=255)

                                                                                          aCGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACcaca                                              >  3:70256/1‑148 (MQ=255)

                                                                                                   aTGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCCGTTTAGCACCAGGTAGTGCCGTTGTCAGGGATTTAGTGAATGTAGAATTATTCTTTGAATCAGATTTACACACATTGCCACcacagt                                            >  2:743/1‑139 (MQ=255)

                                                                                                         ttGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAAt                                      <  1:40165/141‑1 (MQ=255)

                                                                                                           ggTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAg                             >  3:410762/1‑148 (MQ=255)

                                                                                                           ggTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAg                             >  3:289522/1‑148 (MQ=255)

                                                                                                           ggTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAg                             >  4:409965/1‑148 (MQ=255)

                                                                                                                tGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGAc                               <  1:63229/141‑1 (MQ=255)

                                                                                                                tGCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAGATaaa                        <  3:84969/148‑1 (MQ=255)

                                                                                                                ggCCGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACACTGCCACCACATTTTGAATTAAAGAc                               <  1:28621/140‑1 (MQ=255)

                                                                                                                  ccGTTGGTGACACGATGTTTTATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAg                             >  1:21089/1‑141 (MQ=255)

                                                                                                                                    tttATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAGATAAAACACGGGAAATGATGGATTc    <  3:371405/148‑1 (MQ=255)

                                                                                                                                      tATGGAAAAGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAGATAAAACACGGGAAATGATGGATTCAg  >  3:29742/1‑148 (MQ=255)

                                                                                                                                             aaGGGGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAGATAAAACACGGGAAATGATGGATTCAg  >  1:16897/1‑141 (MQ=255)

GAATATATGAAAATGGCAAAGTTAATGCATCGGTAGAACCAACGTTAATTGATAAAAAGCATCAATTAGCAGCTGTAGAGGATGAATATAACGCGATTTATGTTATTGGTGATGCCGTTGGTGACACGATGTTTTATGGAAAAGGAGCAGGCAGTTTAGCAACAGGTAGTGCCGTTGTCAGTGATTTATTGAATGTAGCATTATTCTTTGAATCAGATTTACACACATTGCCACCACATTTTGAATTAAAGACAGATAAAACACGGGAAATGATGGATTCAG  >  USA300TCH1516_ALE/1358091‑1358372

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