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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	411,829	C→T	W218* (TGG→TAG)	araJ ←	L‑arabinose‑inducible putative transporter, MFS family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	411,829	0	C	T	92.3%	65.7 / ‑1.0	26	W218* (TGG→TAG)	araJ	L‑arabinose‑inducible putative transporter, MFS family
Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (16/8); total (17/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.94e-01

AATAACGTCCTGAAATCCTGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACCAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGATTTCCTTTCGCCTCGTCGCGAATATCTGGCACCCAAAAATAGAC  >  NC_000913/411695‑411962

aaTAACGTCCTGAAATCCTGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGc                                                                                                                                   >  1:353887/1‑139 (MQ=255)

     cGTCCTGAAATCCTGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAaca                                                                                                                              >  1:122105/1‑139 (MQ=255)

       tCCTGAAATCCTGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAacaca                                                                                                                            >  2:376251/1‑139 (MQ=255)

       tCCTGAAATCCTGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAacaaa                                                                                                                            >  1:642733/1‑137 (MQ=255)

             aaTCCTGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAAAAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGTAAACACACCTGCg                                                                                                                      <  2:25880/139‑1 (MQ=255)

                  tGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACCAGGCAAACACACCTg                                                                                                                        >  1:190731/1‑132 (MQ=255)

                  tGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACCAGGCAAACACACCTg                                                                                                                        <  2:190731/132‑1 (MQ=255)

                   gCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCa                                                                                                                >  1:167666/1‑139 (MQ=255)

                              tatTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAGACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTg                                                                                                                        <  1:726743/120‑1 (MQ=255)

                              tatTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAGACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTg                                                                                                                        >  2:726743/1‑120 (MQ=255)

                                 ttCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTggcggc                                                                                                  <  1:376251/139‑1 (MQ=255)

                                 ttCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGCCAAACACACCTGCGTTGCCAAACAGCGTggcggc                                                                                                  >  2:515582/1‑139 (MQ=255)

                                        cACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAAtt                                                                                           <  2:122105/139‑1 (MQ=255)

                                             gcccTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCa                                                                                      >  1:502059/2‑139 (MQ=255)

                                                        aCTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGc                                                                           <  2:642733/139‑1 (MQ=255)

                                                        aCTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGc                                                                           >  2:477780/1‑139 (MQ=255)

                                                                             aTCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGtt                                                      >  1:165876/1‑139 (MQ=255)

                                                                                  cGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCgcgc                                                 <  1:282641/139‑1 (MQ=255)

                                                                                     ttCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGa                                              <  2:165876/139‑1 (MQ=255)

                                                                                      tCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCCAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTCAAATTGTTCGCGCAGAt                                             <  2:502059/139‑1 (MQ=255)

                                                                                                             catGTATGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGATTTCCTTTCGCCTCGTCGCGAata                      >  2:31115/1‑139 (MQ=255)

                                                                                                                  aTGGCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGATTTCCTTTCGCCTCGTCGCGAATATCTgg                 >  2:107530/1‑139 (MQ=255)

                                                                                                                    ggCTTTACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGATTTCCTTTCGCCTCGTCGCGAATATCTGGCa               >  1:141465/1‑139 (MQ=255)

                                                                                                                       tttACGTAGCTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGATTTCCTTTCGCCTCGTCGCGAATATCTGGCAccc            >  2:728474/1‑139 (MQ=255)

                                                                                                                                cTGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGATTTCCTTTCGCCTCGTCGCGAATATCTGGCACCCAAAAATAGa   >  1:585343/1‑139 (MQ=255)

                                                                                                                                 tGAACTAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGATTTCCTTTCGCCTCGTCGCGAATATCTGGCACCCAAAAATAGAc  >  2:415958/1‑139 (MQ=255)

AATAACGTCCTGAAATCCTGCCACTTAGCATATTTCCCAGCACCATCCCTAGCCCAACTAACATCATAATAAAGGTCATCGCCGTTTCCGAAAAACCGGAAATAAACATCATGTATGGCTTTACGTAGCTGAACCAGGCAAACACACCTGCGTTGCCAAACATCGTGGCGGCGAAAATTAACCACGGGGCCGGGCTGCGCAAAAAGTGAAATTGTTCGCGCAGATTTCCTTTCGCCTCGTCGCGAATATCTGGCACCCAAAAATAGAC  >  NC_000913/411695‑411962

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A