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
A11 F44 I0 R1	115	55.9	2109214	91.7%	1934149	142.3

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	98.0%	130.3 / ‑6.2	46	noncoding (35/75 nt)	glnX	tRNA‑Gln
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (25/19); minor base G (1/1); total (26/20)
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
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.

TCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGC  >  NC_000913/696332‑696607

tCGCCTCCGACATTGAAGGCTAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGaa                                                                                                                                       <  2:929703/143‑1 (MQ=255)

   cATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGGAGCGAGCTTTTTTAATGTGGCTGGGGTCCGACGAGTCGAAGCTGGGAATGCCGGAAGTAGaaacg                                                                                                                                    >  2:913004/1‑140 (MQ=255)

     tCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCgg                                                                                                                                  >  1:914575/1‑143 (MQ=255)

       cGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGACTTAGAATCCGGTg                                                                                                                                >  1:611176/1‑143 (MQ=255)

       cGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTg                                                                                                                                >  1:278/1‑143 (MQ=255)

        gACATTGAAGGAGAAGACGTGGCAACATCGCATGCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGc                                                                                                                               <  1:92810/143‑1 (MQ=255)

            ttGAAGGATAAGACGTGTCAACATCGCATGCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTa                                                                                                                           <  1:759644/143‑1 (MQ=255)

               aaGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTAccc                                                                                                                        >  2:529509/1‑142 (MQ=255)

                aGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAGCGCTCGCCGAAGCGAGCTTTAGTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGc                                                                                                                       >  1:489441/1‑143 (MQ=37)

                  gATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGATCGCCGAAGCGCGCTTATCAAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCtt                                                                                                                     >  1:771327/1‑143 (MQ=25)

                   aTAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAACAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACGTGGGACCGCAGGAATGAGAATCCGGTGCCTTACCGCTTg                                                                                                                    >  1:438959/1‑143 (MQ=37)

                   aTAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTg                                                                                                                    >  1:450509/1‑143 (MQ=255)

                            gtCAACATCGCGTTCGACATGGAATGAACGCAGAACAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAccc                                                                                                           <  2:505455/143‑1 (MQ=255)

                                 cATCGCATTCCACATTGAATGAACCCAGAAAAGCAAAAAGCTCGCTGAAGCGAGCTTTTTTAAGGTGGCTGGGGTACGATGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACt                                                                                                      <  2:978766/143‑1 (MQ=21)

                                     gCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGt                                                                                                  <  1:520169/143‑1 (MQ=255)

                                        ttCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGTTGCCTTACCGCTTGGCGATCCCCCACCTGGGTGcc                                                                                               >  2:61473/1‑142 (MQ=255)

                                          cGACATTGAATGTACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTGTTAATGTGGCTGGGGTACGAGGATCCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACt                                                                                             <  1:888513/143‑1 (MQ=255)

                                          cGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTCAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACt                                                                                             <  1:889794/143‑1 (MQ=255)

                                                   atgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGGTGCACTTACATgggc                                                                                    >  2:443988/1‑141 (MQ=255)

                                                        cGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGAGTGCACTTACAAGGTCAGCgc                                                                               >  2:824858/1‑142 (MQ=255)

                                                           aGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGGCtt                                                                            >  1:664210/1‑143 (MQ=255)

                                                           aGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTGTAATGTGGCTGGGGTGCGAGGGTTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCtt                                                                            <  1:847944/143‑1 (MQ=255)

                                                             aaaaGCAAAAAGCTCGCCGAAGCGAGCTTTTTTTATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGa                                                                          <  1:968860/143‑1 (MQ=255)

                                                                    aaaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTACGCGCCTCGACTAAAtt                                                                   >  1:814503/1‑143 (MQ=21)

                                                                    aaaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAtt                                                                   <  1:693165/143‑1 (MQ=255)

                                                                     gaaGCTCGCCGAAGCGAGCTTTTGTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTg                                                                  <  2:554811/142‑1 (MQ=255)

                                                                     aaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTg                                                                  >  1:168422/1‑143 (MQ=255)

                                                                      aaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTgg                                                                 <  2:837516/143‑1 (MQ=255)

                                                                         cTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTg                                                              >  1:269962/1‑143 (MQ=255)

                                                                          tCGCCGAAGCGAGCTTTTGTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTgg                                                             <  1:150814/143‑1 (MQ=255)

                                                                             ccGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACATGTTACGCGCCTTGACTCAATTGGCTgaagt                                                          >  2:798836/1‑139 (MQ=21)

                                                                             ccGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGt                                                          >  1:745126/1‑143 (MQ=255)

                                                                               gAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCAGGTGACTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTCAGCGTCTTGAATACATTGGCTGGGGTAc                                                        >  1:425938/1‑143 (MQ=25)

                                                                                    gAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGa                                                   <  2:450509/143‑1 (MQ=255)

                                                                                      gCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGACTGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCCCTTACACGCTACGCCCCTCGAATAACTTCGCTGGCGTCCGAggctc                                                 >  1:254024/1‑140 (MQ=17)

                                                                                          ttttAATGTGGCTGGGGTACGAGGATTCGAACCTAGGAATGCCGGACTTAGAATCCGGTGCCTTACCGCTTGGCGATACAATTTTTTGGTGCACTTACATGGTATGCGTCTTGACTAAATTGGCTGGGGTACGAGGATTCGaa                                             >  1:938049/1‑143 (MQ=18)

                                                                                          tgttAAGGGGGCTGGGGTACGAGGAGTCGAACCGCGGAGTGCCGGAATTGGAATGCGGTGCCTTAGCGCGTGGCGATACCCCAAGTGGGTGCACTTACGGGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGaa                                             <  2:590030/141‑1 (MQ=255)

                                                                                              aaTGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGCTTCGAACCTc                                         >  1:879778/1‑143 (MQ=255)

                                                                                               aTGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCg                                        <  1:616432/143‑1 (MQ=255)

                                                                                                        gggTACGAGGATTCGAACCTCGGAATGCCGGAACTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCgg                               <  1:427852/143‑1 (MQ=255)

                                                                                                        gggTACGAGGACTCGAACCTCGGAATGACGGAATGAGAAACCGGTGCCTTAGCGCTTGGCGATACCCCGACTGGGGGCACGTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCgg                               <  2:281138/143‑1 (MQ=38)

                                                                                                             cGAGTATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCa                          <  1:408419/143‑1 (MQ=255)

                                                                                                                      gAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTAGGTGGACTTGCATGGTCAGCGCCTAGACTAAATCGGCAGAGTTACGAGGATTCGACCATCGGAAAGCCGGTAACAGCATcctga                 >  2:284808/1‑140 (MQ=12)

                                                                                                                        aCCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTACGCGTCTTGCATAAATTGCCTGGGGTACGAGGCTTCGAACCCCGGAATGACGGCATCAGAATACGGTGc               >  2:518338/1‑143 (MQ=25)

                                                                                                                                   ccGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGCCTAAATTGGCTGGCGTACGAGGCTTCGAACCTCGGAATGCCGGTATCAGGATCCGGtgccgtgccgtgtg    >  2:726981/1‑139 (MQ=37)

                                                                                                                                     ggAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGc  >  2:1021582/1‑143 (MQ=255)

TCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGC  >  NC_000913/696332‑696607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A