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
A19 F91 I0 R1	49	33.8	1296440	89.8%	1164203	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	696,470	C→T	100%	noncoding (35/75 nt)	glnX ←	tRNA‑Gln

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	696,470	0	C	T	100.0%	87.2 / ‑6.7	32	noncoding (35/75 nt)	glnX	tRNA‑Gln
Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (18/13); total (19/13)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAG  >  NC_000913/696338‑696584

ccGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCAGGAATTTGAATCCGGt                                                                                                          >  1:398808/1‑143 (MQ=255)

 cGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGGACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTg                                                                                                         >  1:41523/1‑143 (MQ=255)

  gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGc                                                                                                        >  1:79593/1‑143 (MQ=255)

       tGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGTATGCCGGAATTAGGATCCGGTGCCTTAc                                                                                                   >  2:374373/1‑143 (MQ=255)

       tGAAGGATAAGACGTGGCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAGGCCCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTAc                                                                                                   <  2:225425/143‑1 (MQ=255)

                    gtgtCAACATCGCATGCGACATTTAAGGAACGCAGACAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTACTGTGGCTGCGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAc                                                                                      <  2:612364/143‑1 (MQ=25)

                      gtCAACATCGCATTCGACATTGAATGAACGCGGAAAAGCAAAAAGCTCGCCGACGCGAGCGTTTTTAATGTGGCTGGGGCACGAGGATTCGAACCTCGGAAAGCCCGAGTCAGAATCCGGTGCCTTACCGCTGGGCGCTGccc                                                                                    >  2:429995/1‑143 (MQ=25)

                             tCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTgg                                                                             <  1:485394/143‑1 (MQ=255)

                              cGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTggg                                                                            >  1:320188/1‑143 (MQ=255)

                               gCATTCGACCGTGAATGAACGCAGAAAAGGAAAAAGCTCGCCGAAGCGAGCTTTTGTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAAGCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGt                                                                           <  2:117867/143‑1 (MQ=21)

                               gCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGt                                                                           <  2:124055/143‑1 (MQ=255)

                                cATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACGGGGTg                                                                          >  1:135674/1‑143 (MQ=255)

                                     gACATTGAATGTACGCACAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACtt                                                                     <  1:163408/143‑1 (MQ=255)

                                         ttGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACaa                                                                 >  1:415442/1‑143 (MQ=255)

                                                     aGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCAAACTGGGTGCACTTACAAGGTAAGCGTCtt                                                     <  2:79593/143‑1 (MQ=255)

                                                       aaaaGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGa                                                   >  1:20033/1‑143 (MQ=255)

                                                            cAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGCATCCGGTGCCTTACTGCTTGGCGATACCCCAACTGCGTGCACTTACCAGTTAACCGCATAGAATaaa                                              >  2:373593/1‑143 (MQ=21)

                                                            cAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATaaa                                              >  1:444361/1‑143 (MQ=255)

                                                            cAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGCCGATACCCCAACTGGGTGCTCTTACAACGTCACCACCTTGAATaca                                              >  2:88085/1‑141 (MQ=21)

                                                             aaaaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAt                                             <  1:586334/143‑1 (MQ=255)

                                                             aaaaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAt                                             <  2:415442/143‑1 (MQ=255)

                                                                    tCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTgg                                      >  1:40993/1‑143 (MQ=255)

                                                                           aGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTGCAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGa                               >  1:562357/1‑143 (MQ=255)

                                                                              gAGCTGTTAGAACGTGGCTGGGGCACGAGGATTCGAACCCCGGAATGCCGGAATTAGAGTCCGGGGCCTTACCGCTTGGCGCTACCCCAACTGGCTGCACTGATAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGa                            <  1:374373/143‑1 (MQ=255)

                                                                                  ttttttAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGGACTTGCAAGGTAAGCGTATTGAATAAATTGGCTGGGGTACGAGGATTCg                        >  1:468233/1‑143 (MQ=255)

                                                                                    ttttAATGTGGCTGGTGTACGAGGATTCGAAGTTCGGAATGCCGTAATTAGAATCCGGTGCATTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGaa                      <  1:341765/143‑1 (MQ=37)

                                                                                    ttttAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATTCGGTGCCTTACCGCTGGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGaa                      <  1:341242/143‑1 (MQ=255)

                                                                                    agtcaaTGAGGCTGGGGTACATGGTGTCGAGCCACGGAATGCCGAAATTAGAATCCATTGCCTTAGCGCTTGGCGATACCCCAACTGGGTGCAATCACGAGGTAACCGGCTTGAATAAAGTGGCTGGGGTACGAGGATTCGaa                      <  2:353128/139‑1 (MQ=255)

                                                                                     tatAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAAACCGGTGCCTTACCTCTTGGCGATACCCCAACTGGGTGCACTTAGACGGTAGGCGGCCTGAATAAATAGGATGGGGTACGAGGATTAGAAc                     >  1:287840/3‑143 (MQ=18)

                                                                                       tactgtgGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCGTGGCGATACCCCAACTGGGTGCATTTACATGGGACGCGTCTAGAATAAATAGGCGGGGGTACGCGGCTTCGacgcg                   >  2:619331/4‑139 (MQ=17)

                                                                                          tgtgGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGGACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGGTTCGAACCTCgg                >  1:299675/1‑143 (MQ=255)

                                                                                                        gAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGGACTTGCAAGTTAAGCATCTAGAATAAATTGGCAGGCGTACGCGGCTTCGACCCTCGTAGAGCCTGAATccg  >  2:4898/1‑141 (MQ=18)

CCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAG  >  NC_000913/696338‑696584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A