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 F83 I0 R1	128	58.1	2217184	91.0%	2017637	142.6

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	96.4%	114.7 / ‑4.2	42	noncoding (35/75 nt)	glnX	tRNA‑Gln
Reads supporting (aligned to +/- strand): ref base C (0/2); new base T (24/15); total (24/18)
Fisher's exact test for biased strand distribution p-value = 1.66e-01
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.

CGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGC  >  NC_000913/696333‑696607

cGCATCCGACATTGAAGGATACGACGTGGCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGTAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAAt                                                                                                                                       <  2:641036/143‑1 (MQ=255)

  cATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATcc                                                                                                                                     >  1:581377/1‑143 (MQ=255)

      cGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTg                                                                                                                                 >  1:530632/1‑143 (MQ=255)

       gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTGGAATCCGGGGc                                                                                                                                >  1:420552/1‑143 (MQ=255)

             gAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCGGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTAcc                                                                                                                          >  1:630309/1‑143 (MQ=255)

              aaGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCg                                                                                                                         >  1:975939/1‑143 (MQ=255)

              aaGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCg                                                                                                                         >  1:871358/1‑143 (MQ=255)

                 gATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGGGGGTGGGGTGCGAGGATGCGAACCTCGGAATGCCGGCATTCGAATCCGGTGGCGGACCGCtt                                                                                                                      >  1:373592/1‑143 (MQ=255)

                       aCGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGAt                                                                                                                >  2:1088089/1‑143 (MQ=255)

                        cGTGTCAACGTCGCATTCGTCATTGAATGATCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATa                                                                                                               <  2:698819/143‑1 (MQ=255)

                           gtcgagaTCTCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTGGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAccc                                                                                                            <  2:946801/137‑1 (MQ=25)

                            tCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAACCCGGTGCCGTACAGCATGGCAAtcgcgc                                                                                                           >  2:712627/1‑138 (MQ=37)

                                    gCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGt                                                                                                   <  2:1043568/143‑1 (MQ=255)

                                       ttCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGCGGATTCGAACCTCGGAATGGAGGAATTAAAATCCGGTGCCTTGCCGCTTGGCGATACCCCAACTGGGTGCa                                                                                                >  1:42253/1‑143 (MQ=37)

                                        tCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCACCGGGGTGCAc                                                                                               >  1:385302/1‑143 (MQ=255)

                                        gcgtctttGTATGGACTCAGAAGAGCAATACGTTGGCCGAAGCGAGCTTTTTTAATGCGGGTGGTGTACGAGGGTTCGAGCCTCGGAATGCCGGATTTAGTATCCGGTGCCTTACCGCTTGGCGATACCCCAAATGGGTGCAc                                                                                               <  2:849075/137‑1 (MQ=12)

                                               tgaatgagCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAg                                                                                        <  2:796179/143‑1 (MQ=255)

                                               cgcaggaaCGCACAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAg                                                                                        <  2:420552/138‑1 (MQ=255)

                                                  atgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACCAGGTa                                                                                     >  1:152778/1‑143 (MQ=255)

                                                  atgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACCGGGTGCACTTACAAGGTa                                                                                     >  2:235804/1‑143 (MQ=255)

                                                      aCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTAGAAGGtgcgcg                                                                                 >  2:1002714/1‑138 (MQ=255)

                                                            aaaaGCAAAAAGCTCGCCGAAGCGAGCTTGTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGa                                                                           <  1:781181/143‑1 (MQ=255)

                                                             aaaGCAAGAAGCTCGCCGAAGCGTGCTTTTTTAATGTGGCTGGGGTTCGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGaa                                                                          <  2:638239/143‑1 (MQ=255)

                                                                    catggtCGCCGAAGCGAGCTTGTTTAATGTGGCTGGGGTACGAGGTTTCGAACCTCGGAATGCCGGGATTAGATTCCGGTGCCTTACCGCTTGGCGATACCCCAACTGCGTGCACTTACTAGGTAAGCGTCTTGAATAAAT‑Tg                                                                  <  2:334205/138‑1 (MQ=21)

                                                                         tCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTgg                                                             >  1:434736/1‑143 (MQ=255)

                                                                           gCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAAGGTGCACTTGCACTGTAAGCGCCCTGGAGCAAT‑GGGCTggga                                                           >  2:583145/1‑142 (MQ=17)

                                                                              gAAGCGATCTGTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGTACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTAc                                                        <  2:775295/143‑1 (MQ=255)

                                                                              gAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGACTAAAG‑TGGCTGGGGTAc                                                        >  1:428709/1‑143 (MQ=255)

                                                                                    agctgcgttAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGAt                                                  <  1:601434/136‑1 (MQ=255)

                                                                                    aGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAAGGAGAATCCGGTGCCTGACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGAt                                                  <  1:251140/143‑1 (MQ=255)

                                                                                         ttttAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCaa                                                                                                         >  1:396536/1‑84 (MQ=255)

                                                                                         ttttAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCaa                                                                                                         <  2:396536/84‑1 (MQ=40)

                                                                                             actgtgGATGGGGTACGTGGATTCGAACCTCGCAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGATTCGAACCTc                                         <  2:530632/141‑1 (MQ=255)

                                                                                                   gCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGATTCGACCCTCGGAATg                                   >  1:289575/1‑143 (MQ=255)

                                                                                                           aCGGGGACTCGAACCGCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATc                           <  1:857711/143‑1 (MQ=255)

                                                                                                           aCGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGCTTCGAACCTCGGAATGCCCGAGTc                           >  1:407404/1‑143 (MQ=255)

                                                                                                              aGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGCTTCGACCCGCGGCATGCCGCAACCAGa                        >  1:401230/1‑143 (MQ=25)

                                                                                                                 atgcGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGGTGCACTTGCAAGGTCCGCGCATTGAATAAAT‑TGGCTGAGGTACGAGGATCCGACCGTCGGAATACCGGTGTCCGAATc                     >  2:400339/4‑143 (MQ=18)

                                                                                                                     gagccTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGt                 <  1:231340/140‑1 (MQ=255)

                                                                                                                                   cGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTgg   <  1:781757/143‑1 (MQ=255)

                                                                                                                                    ggAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGGTGCACTTACAAGGTAAGAGTCTTGAATAAAT‑TGGCGGGGGTACGAGGATACGAACCTCGGAATACCGGAATCCGAATCCGCACACTTACCGccaggc  >  2:819818/1‑138 (MQ=25)

                                                                                                                                    ggAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGCTGCACTTACACGGCAAGCGCGTCGAATAAATCTGGC‑GGAGTGCGAGGATACGAACCTCGGAAAGCCGGAATCAGACTGCGGTGACCTCCCGCGTGGc  >  2:596548/1‑143 (MQ=16)

CGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAT‑TGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGC  >  NC_000913/696333‑696607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A