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
A9 F28 I1 R1	120	56.0	1898522	99.4%	1887130	138.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,237,673	(G)_5→6	coding (103/1299 nt)	dadA →	D‑amino acid dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,237,668	1	.	G	97.6%	139.3 / ‑3.2	41	coding (98/1299 nt)	dadA	D‑amino acid dehydrogenase
Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (25/15); total (26/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.63e-01

ATTATTATTCTTTTACTGTATCTACCGTTATCGGAGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCC‑GGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTAAAAGCGATTAAATGGATGTTCCAGCGCCATGCGCCGCTGGCGGTT  >  NC_000913/1237530‑1237801

attattattCTTTTACTGTATCTACCGTTATCGGAGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCATCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCC‑g                                                                                                                                      >  2:817367/1‑140 (MQ=255)

     tattCTTTTACTGTATCTACCGTTATCGGAGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCC‑gggggg                                                                                                                                 <  2:498251/140‑2 (MQ=255)

     tattCTTTTACTGTATCTACCGTTATCGGAGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCC‑gggggg                                                                                                                                 <  1:62288/140‑2 (MQ=255)

            ttACTGTATCTACCGTTATCGGAGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCt                                                                                                                           >  2:519725/1‑140 (MQ=255)

                 gTATCTACCGTTATCGGAGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGaaa                                                                                                                      >  2:137834/1‑140 (MQ=255)

                    tCTACCGTTATCGGAGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCa                                                                                                                   >  1:52025/1‑140 (MQ=255)

                                  aGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGcc                                                                                                     >  1:164900/1‑140 (MQ=255)

                                      gCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCGGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGc                                                                                                 >  2:648955/1‑140 (MQ=255)

                                            cGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAAtct                                                                                           >  1:471799/1‑140 (MQ=255)

                                                ttGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTcccc                                                                                       >  2:177187/1‑140 (MQ=255)

                                                ttGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTcccc                                                                                       >  1:199577/1‑140 (MQ=255)

                                                ttGTCATACTGGGAAGTGGTGAGGTAGGCGGTGCCAGCGCCTGGCACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGGGCCGCGAATGCCGGGCAAATCTcccc                                                                                       >  2:163360/1‑140 (MQ=255)

                                                     aTACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCggg                                                                                                  >  1:578157/1‑124 (MQ=255)

                                                     aTACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCggg                                                                                                  <  2:578157/124‑1 (MQ=255)

                                                     aTACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGat                                                                                  <  1:519725/140‑1 (MQ=255)

                                                           ggAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATAtgctg                                                                            >  1:622272/1‑140 (MQ=255)

                                                           ggAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATAtgctg                                                                            >  2:697588/1‑140 (MQ=255)

                                                                tggtgtggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCg                                                                       >  1:113623/1‑140 (MQ=255)

                                                                  gtgtggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTg                                                                     >  2:806152/1‑140 (MQ=255)

                                                                  gtgtggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTg                                                                     >  1:570264/1‑140 (MQ=255)

                                                                  gtgtggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTg                                                                     >  2:83245/1‑140 (MQ=255)

                                                                   tgtggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTgg                                                                    >  2:476684/1‑140 (MQ=255)

                                                                    gtggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTggg                                                                   <  2:622272/140‑1 (MQ=255)

                                                                    gtggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTggg                                                                   <  2:164900/140‑1 (MQ=255)

                                                                     tggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGggc                                                                  <  2:764716/140‑1 (MQ=255)

                                                                     tggtAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGggc                                                                  >  1:565313/1‑140 (MQ=255)

                                                                        tAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCAcc                                                                        <  1:45205/131‑1 (MQ=255)

                                                                        tAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCAcc                                                                        >  2:45205/1‑131 (MQ=255)

                                                                               tGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCa                                                              <  1:139329/134‑1 (MQ=255)

                                                                               tGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCa                                                              >  2:139329/1‑134 (MQ=255)

                                                                               tGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGgt                                                        <  1:697588/140‑1 (MQ=255)

                                                                               tGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGgt                                                        >  1:229561/1‑140 (MQ=255)

                                                                               tGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGgt                                                        <  2:910789/140‑1 (MQ=255)

                                                                                 ccAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTTATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGgtgt                                                      <  1:817367/140‑1 (MQ=255)

                                                                                 ccAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCC‑GGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGtgtg                                                     >  1:915485/1‑140 (MQ=255)

                                                                                           gTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTaaaa                                            <  2:471799/140‑1 (MQ=255)

                                                                                           gTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTaaaa                                            <  2:199577/140‑1 (MQ=255)

                                                                                                      aggcaggACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTAAAAGCGATTAAATg                                 >  2:689394/1‑140 (MQ=255)

                                                                                                            gACATGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTAAAAGCGATTAAATGGATGtt                           >  1:842205/1‑140 (MQ=255)

                                                                                                               aTGAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTAAAAGCGATTAAATGGATGTTCCa                        <  2:842205/140‑1 (MQ=255)

                                                                                                                 gAGGTCACCGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTAAAAGCGATTAAATGGATGTTCCAgc                      <  1:83245/140‑1 (MQ=255)

                                                                                                                        ccGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTAAAAGCGATTAAATGGATGTTCCAGCGCCATgc               >  1:45909/1‑140 (MQ=255)

                                                                                                                         cGTCATTGATCGGGAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTAAAAGCGATTAAATGGATGTTCCAGCGCCATgcg              >  2:103438/1‑140 (MQ=255)

                                                                                                                                     ggAGCCGGGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTTAAAGCGATTAAATGGATGTTCCAGCGCCATGCGCCGCTGGCGGtt  <  2:558881/140‑1 (MQ=255)

ATTATTATTCTTTTACTGTATCTACCGTTATCGGAGTGGCTATGCGAGTTGTCATACTGGGAAGTGGTGTGGTAGGCGTTGCCAGCGCCTGGTACTTAAATCAGGCAGGACATGAGGTCACCGTCATTGATCGGGAGCC‑GGGGGCCGCCCTGGAAACCAGTGCCGCGAATGCCGGGCAAATCTCCCCCGGATATGCTGCACCGTGGGCGGCACCAGGTGTGCCTTTAAAAGCGATTAAATGGATGTTCCAGCGCCATGCGCCGCTGGCGGTT  >  NC_000913/1237530‑1237801

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A