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
A25 F66 I1 R1	21	40.5	1611144	86.0%	1385583	142.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	696,470	C→T	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	96.9%	74.1 / NA	32	noncoding (35/75 nt)	glnX	tRNA‑Gln
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (13/18); minor base G (0/1); total (13/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTG  >  NC_000913/696337‑696605

tCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGACTTAGAATCggg                                                                                                                                >  1:243659/1‑143 (MQ=255)

 ccGACATTGATGCACAAGACGTGGTAACATCGTATTCGACATTGAATGATCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGt                                                                                                                               <  2:494795/143‑1 (MQ=37)

     cATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCGCGCCGAAGCGAGCTTTGTTAATGTGGTTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCt                                                                                                                           <  2:173488/143‑1 (MQ=255)

     cATTGAAGGATAAGACGTGTCAAAATCGTATGCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCt                                                                                                                           <  1:446626/143‑1 (MQ=255)

         gAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGAAATGCCGGAATTAGAATCCGGTGACTTAcc                                                                                                                       >  1:700366/1‑143 (MQ=255)

          agggcgaaGACGTGTGAACATCGCATTCGACATTGAATTAACGCAGAAAAGCAAAAAGCTCGCTGAAGCGAGCTTTTTTAATGTGGCTGGGGTACTAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCg                                                                                                                      <  2:33663/137‑1 (MQ=37)

             gATAAGACGTGTCAACATCGCATTCGACATTGTATGAACGCAGAAAAGCAACAAGCTCGGCGAAGCGCGCTTTTTTAATGTGGCTGGGGGACGAGGATTCGAGCCTCGGAATACCGGAATTAGCATCCGGGGCCTTAcccatc                                                                                                                   >  2:411064/1‑139 (MQ=255)

               caaGACGTGTCAACATCGCCTTCGACATTGAATGCACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATTTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTgg                                                                                                                 <  2:716158/142‑1 (MQ=255)

                     gtgtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGCAATGCCGGAATTCGAGACCGTTGCAGTACCGCTTGGCGATaa                                                                                                           >  2:516056/1‑142 (MQ=37)

                      tgtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAcc                                                                                                          <  1:531444/143‑1 (MQ=255)

                          aaCATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACACCaa                                                                                                      >  2:398572/1‑143 (MQ=255)

                              tCGCATTGGATATCGTATGGACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCGGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTgg                                                                                                  <  2:520912/143‑1 (MQ=21)

                              tCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTgg                                                                                                  >  1:473091/1‑143 (MQ=255)

                               cGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTggg                                                                                                 <  1:711400/143‑1 (MQ=255)

                                      gACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTGCCGCTTGGCGATACCCCAAATGGGTggattt                                                                                          >  2:802544/1‑138 (MQ=255)

                                       aCATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGGTGCACTTa                                                                                         >  2:708667/1‑143 (MQ=255)

                                               tgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTaa                                                                                 <  2:547545/143‑1 (MQ=255)

                                                    gCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACTAGGATTCGAACCTCGGAATGCCGAAATTAGAATCCGGGGGCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTc                                                                            <  1:216080/143‑1 (MQ=37)

                                                     cAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGGTGCACTTGCAAGGGACGCGCCt                                                                           >  2:704297/1‑143 (MQ=21)

                                                             cAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGTGGTACGAGGATTCGAACCGCGGAATGCCGGAATTAGAATAAGGTGCCTTAACGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATaaa                                                                   >  1:565953/1‑143 (MQ=37)

                                                             cAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGGTGAACTTACAAGGTAAGCGCCTTGAATaaa                                                                   >  2:255853/1‑143 (MQ=255)

                                                                      cGCCGACGCGAGCTTGTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCATTACGGCTTGGGGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTggg                                                          <  1:190111/143‑1 (MQ=25)

                                                                       gCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTgggg                                                         >  1:670397/1‑143 (MQ=255)

                                                                                  cTTTTTTAATGTGGCTTGGGTACGAGGATTCGAACCTCGGAAAGCCGGAAGGAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTc                                              <  1:310744/143‑1 (MQ=255)

                                                                                    tttggagtgtgGCTGGGGTACGGGGATTCGAACCGCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGa                                            <  2:133625/136‑1 (MQ=25)

                                                                                      tgtAATGTTGTTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAAGCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAAc                                          <  2:521533/141‑1 (MQ=255)

                                                                                                  ggggTACGAGGATTCGAACCTCGGAATGCCGGAATTATAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTAGGTGCACTTACAAGGTACGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCGCGGAATGCCg                              >  2:203894/1‑143 (MQ=25)

                                                                                                      tACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAAt                          <  1:574368/143‑1 (MQ=255)

                                                                                                               gctccccTCGGAATGCCGGAATTAGACTCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCg                 <  2:771704/138‑1 (MQ=255)

                                                                                                                cGAACCTCGGAATGCCGGAATTAGATTCCGGTGCCTTACTGTTTGGTGATACTTCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCgg                <  1:602261/143‑1 (MQ=37)

                                                                                                                 gtaCCTCGGACTGCCGGCGTTATACTCCGGCCCCTTACCGCTTGGCGATACCCCAATTCGGTGCACTTACACGGTATGCGTCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGt               <  2:633759/141‑1 (MQ=17)

                                                                                                                              tcagAATTAGAATTCGGTGCCTTTCCGTTTGGCGATACCCCAACTGGGTGCACGTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTg  <  1:56524/140‑1 (MQ=25)

TCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTG  >  NC_000913/696337‑696605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A