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 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	60,719	C→T	G849D (GGC→GAC)	rapA ←	RNA polymerase‑binding ATPase and RNAP recycling factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	60,719	0	C	T	92.1%	102.0 / ‑1.1	38	G849D (GGC→GAC)	rapA	RNA polymerase‑binding ATPase and RNAP recycling factor
Reads supporting (aligned to +/- strand): ref base C (1/2); new base T (15/20); total (16/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAACGCTTTGTTTTTTAA  >  NC_000913/60585‑60855

gcgcTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGttt                                                                                                                                     >  2:144794/1‑140 (MQ=255)

gcgcTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGGTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGttt                                                                                                                                     >  1:813561/1‑140 (MQ=255)

     tCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATc                                                                                                                                <  1:835139/140‑1 (MQ=255)

         ccAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCcagc                                                                                                                            <  1:144794/140‑1 (MQ=255)

         ccAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCcagc                                                                                                                            <  2:746847/140‑1 (MQ=255)

            gTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCagcagc                                                                                                                         <  2:656308/140‑1 (MQ=255)

            gTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCagcagc                                                                                                                         <  1:2741/140‑1 (MQ=255)

                      aGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCCGCAGCATACGTAccc                                                                                                               >  2:332043/1‑139 (MQ=255)

                       gCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCgg                                                                                                              >  1:359848/1‑140 (MQ=255)

                       gCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGGTGTTGTCGTTTTTATCCAGCAGCATACGTAcccg                                                                                                              >  2:532130/1‑138 (MQ=255)

                       gCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGGTTTAAAATATTCCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCTGCAGCATACGTATCgg                                                                                                              >  2:782383/1‑140 (MQ=255)

                       gCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGGTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCgg                                                                                                              >  1:792099/1‑140 (MQ=255)

                                  ctgctgCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCa                                                                                                   >  2:479981/1‑140 (MQ=255)

                                  ctgctgCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAACGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCa                                                                                                   <  2:776486/140‑1 (MQ=255)

                                           ggCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGt                                                                                          <  2:525448/140‑1 (MQ=255)

                                           ggCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGt                                                                                          <  2:138415/140‑1 (MQ=255)

                                                       tttGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACt                                                                              <  1:479981/140‑1 (MQ=255)

                                                            tgcCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGGTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTc                                                                         >  2:161087/1‑140 (MQ=255)

                                                                  tgtgACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGcc                                                                   <  2:500862/140‑1 (MQ=255)

                                                                   gtgACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCt                                                                  <  2:813561/140‑1 (MQ=255)

                                                                   gtgACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCt                                                                  <  1:541967/140‑1 (MQ=255)

                                                                            aaCCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCaa                                                         <  1:845863/140‑1 (MQ=255)

                                                                            aaCCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCaa                                                         >  1:291808/1‑140 (MQ=255)

                                                                            aaCCGCGTTAAGCTGGCGGTTAAAGGGTTCAAACTCTACCTGCGCCGCCAGGGTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCaa                                                         >  1:824137/1‑140 (MQ=255)

                                                                              ccGCGTTAAGCTGGCGGTTAAAGGGTTTAAACTCTACCTGCGCCGCCCGGGTGTTGTCGTTTTTTTCCAGCAGCATACGTACCCGCGTCGGGGGGAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCCGGGCTTCAAcc                                                       >  2:429368/1‑140 (MQ=255)

                                                                                 cgTTAAGCTGGCGGTTAAAAGGTTTAAACTCTACCCGCGCCGCCCGGGTGTTGTCGTTTTTTTCCAGCAGCATACGTACCCGCGGCGGTGGCAGGAAGCGGTTTAGCTGCAACTGCTTCGGAGCCCGGGGTTCAACccca                                                    >  2:222121/1‑140 (MQ=255)

                                                                                          ggCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGt                                           <  2:595562/140‑1 (MQ=255)

                                                                                          ggCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGt                                           <  1:429368/140‑1 (MQ=255)

                                                                                          ggCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGCTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGt                                           <  2:797497/140‑1 (MQ=255)

                                                                                            cGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTc                                         <  2:291808/140‑1 (MQ=255)

                                                                                                tAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTccacc                                     <  2:359848/140‑1 (MQ=255)

                                                                                                 aaaGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTccacca                                    <  1:194480/140‑1 (MQ=255)

                                                                                                   aGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAAc                                  <  1:222121/140‑1 (MQ=255)

                                                                                                       ttCAAACTCTACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCg                              <  2:581495/140‑1 (MQ=255)

                                                                                                                tACCTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCg                     >  1:812042/1‑140 (MQ=255)

                                                                                                                  ccTGCGCCGCCAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGc                   >  1:292403/1‑140 (MQ=255)

                                                                                                                        ccgccAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAACGCt             >  2:75307/1‑140 (MQ=255)

                                                                                                                        ccgccAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAACGCt             >  2:214906/1‑140 (MQ=255)

                                                                                                                           ccAGGTTGTTGTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAACGCTTTg          >  1:586822/1‑140 (MQ=255)

                                                                                                                                   ttgTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAACGCTTTGTTTTTTaa  <  1:42665/140‑1 (MQ=255)

                                                                                                                                   ttgTCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAACGCTTTGTTTTTTaa  >  2:462392/1‑140 (MQ=255)

GCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAACGCTTTGTTTTTTAA  >  NC_000913/60585‑60855

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A