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
A14 F1 I1 R1	770	68.5	3470224	91.7%	3182195	103.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,433,164	C→T	287 (TAG→TAA)	qorB ←	NAD(P)H:quinone oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,433,164	0	C	T	100.0%	95.0 / NA	30	287 (TAG→TAA)	qorB	NAD(P)H:quinone oxidoreductase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (14/16); total (14/16)

GGCGTACAGCACGCCGCTAATCATTACTGGCATCCATTGATCTGTCAGAAGAAAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAACTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGCTGTCATCAAACAGACCGCCTTTCGATGCGCCAACGTCAGAA  >  NC_000913/4433033‑4433287

ggCGTACAGCACGCCGCTAATCATTACTGGCATCCATTGATCTGTCAGAAGAAAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGttat                                                                                                                      <  1:282321/139‑1 (MQ=255)

   gTACAGCACGCCGCTAATCATTACTGGCATCCATTGATCTGTCAGAAGAAAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTaa                                                                                                                   >  2:504218/1‑139 (MQ=255)

             ccgcTAATCATTACTGGCATCCATTGATCTGTCAGAAGAAAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAg                                                                                                         <  2:484302/139‑1 (MQ=255)

                    tCATTACTGGCATCCATTGATCTGTCAGAAGAAAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCtt                                                                                                  <  2:766482/139‑1 (MQ=255)

                                    ttGATCTGTCAGAAGAAAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACg                                                                                  <  1:504218/139‑1 (MQ=255)

                                                 agaaAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCt                                                                                                   <  2:1064283/109‑1 (MQ=255)

                                                 agaaAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCtt                                                                                            <  2:457392/116‑1 (MQ=255)

                                                 agaaAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCtt                                                                                            >  1:457392/1‑116 (MQ=255)

                                                 agaaAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGCCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCt                                                                                                   >  1:1064283/1‑109 (MQ=255)

                                                      gTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGttatta                                                                                                                    <  2:450674/87‑1 (MQ=255)

                                                      gTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGttatta                                                                                                                    <  2:614515/87‑1 (MQ=255)

                                                      gTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGttatta                                                                                                                    >  1:614515/1‑87 (MQ=255)

                                                      gTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGttatta                                                                                                                    >  1:450674/1‑87 (MQ=255)

                                                                             tCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGttatta                                                                                                                    <  2:839471/64‑1 (MQ=255)

                                                                             tCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGttatta                                                                                                                    >  1:839471/1‑64 (MQ=255)

                                                                             tCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGTTGGCCAATCAATTTGCt                                                      >  1:1456928/1‑126 (MQ=255)

                                                                             tCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGTTGGCCAATCAATTTGCt                                                      <  2:1456928/126‑1 (MQ=255)

                                                                                       ccGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTaaa                                                                                                            >  2:1359771/1‑62 (MQ=255)

                                                                                       ccGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTaaa                                                                                                            <  1:1359771/62‑1 (MQ=255)

                                                                                                tCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACg                                                                                  >  1:1339360/1‑79 (MQ=255)

                                                                                                tCAGAGAGGATGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACg                                                                                  <  2:1339360/79‑1 (MQ=255)

                                                                                                          tGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCcaatc                                                              <  1:734906/89‑1 (MQ=255)

                                                                                                          tGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGCTGTCATCAAACAGACCGCCTTTCGATGCGcc            >  2:16820/1‑139 (MQ=255)

                                                                                                          tGCGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTGGTCGTTGGGTGGCcaatc                                                              >  2:734906/1‑89 (MQ=255)

                                                                                                            cGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGCTGTCATCAAACAGACCg                          >  2:480254/1‑123 (MQ=255)

                                                                                                            cGGGAGGATGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGCTGTCATCAAACAGACCg                          <  1:480254/123‑1 (MQ=255)

                                                                                                              ggaggaTGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACg                                                                                  <  1:714923/65‑1 (MQ=255)

                                                                                                              ggaggaTGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACg                                                                                  >  2:714923/1‑65 (MQ=255)

                                                                                                               gaggaTGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGCTGTCATCAAACAGACCGCCTTTCGATGCGCCAACGt       <  2:629390/139‑1 (MQ=255)

                                                                                                                    tGCCACTTTAATTAATTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGCTGTCATCAAACAGACCGCCTTTCGATGCGCCAACGTCAGaa  >  2:931401/1‑139 (MQ=255)

                                                                                                                            taattaatTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGc                                           >  2:593240/1‑90 (MQ=255)

                                                                                                                            taattaatTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGc                                           <  1:593240/90‑1 (MQ=255)

GGCGTACAGCACGCCGCTAATCATTACTGGCATCCATTGATCTGTCAGAAGAAAGTTCAGGAAGCAGACATGATTGCTCCCGGCATCCCGTCATTATCAGAGAGGATGCGGGAGGATGCCACTTTAATTAACTAGTTATTAACATTAAAAAGATGGCTTACGCTTTCGGCTAACGTTGTCGTTGGGTGGCCAATCAATTTGCTAAGTGTTTTGCTGTCATCAAACAGACCGCCTTTCGATGCGCCAACGTCAGAA  >  NC_000913/4433033‑4433287

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A