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
A17 F61 I0 R1	36	35.4	1352518	90.1%	1218618	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	98.9%	90.2 / ‑6.5	39	noncoding (35/75 nt)	glnX	tRNA‑Gln
Reads supporting (aligned to +/- strand): ref base C (1/0); major base T (13/24); minor base G (0/1); total (14/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01
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.

CGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCT  >  NC_000913/696330‑696603

cGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCACGCAATTGCGGAATTAg                                                                                                                                     >  2:397738/1‑143 (MQ=255)

   ggCATCCGACATTGAAGGGTAAGGCGTGTCAACATCGCATTCGACATTGAATGAGCGCAGAAAAGCAAGAAGCTCGTCGTAGCGAGCTTGTGTAATGTGGCTGGGGTACGGGGATTCGAACCTCGGAATGCCGGAATTAGAAt                                                                                                                                  <  2:452693/142‑1 (MQ=37)

    gCATCCGACATTGAAGGATAAGACGTGTCAACATCGTCTCCAACATTTAATGAACGCCGATAAGCGATGAGCTCGCCGAAGCGAGCTTTTTTAATGTTGCTGTGGTACGAGTATTCGAACCTCGGAATGCCGGAATTAGAATc                                                                                                                                 <  1:601716/143‑1 (MQ=25)

      ctCCGACACTGAAGTATAAGACGTGTCAACATCCCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCg                                                                                                                               <  1:108608/142‑1 (MQ=255)

      aTCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGCTATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGACCCTCCGAATGCCGGAATCAGAAGCCg                                                                                                                               >  2:480386/1‑143 (MQ=39)

          gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGc                                                                                                                           <  1:171130/143‑1 (MQ=255)

            cATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCt                                                                                                                         >  2:252938/1‑143 (MQ=255)

                 aaGGATTAGACTTGTCAACATCGCATTCGACATTGAATGTACGCAGTAAACCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGTTGTGGTACTAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCg                                                                                                                    <  2:620664/143‑1 (MQ=37)

                                 aaCATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCaa                                                                                                    <  2:499350/143‑1 (MQ=255)

                                 aaCATCGCATTCGACATTGAATGAACACAAAACAGCGAAAAGCTCGCCGACGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCaa                                                                                                    >  1:642505/1‑143 (MQ=21)

                                   cATCGCGTTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACt                                                                                                  <  1:194/143‑1 (MQ=255)

                                   cATCGCATTCGACCTGGAGTGATCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCGTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCGCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACt                                                                                                  <  1:19024/143‑1 (MQ=21)

                                   cATCGCATTCGACATTGAATGAACGAAGAACAGCAAAAAGCGCTCTGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACt                                                                                                  >  1:345877/1‑143 (MQ=21)

                                   cATCGCATGCGACATCGAATGAAGCCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTTGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAAAACAGAGCCTTACCGCTTGGCGATACCCCAACt                                                                                                  <  2:590689/143‑1 (MQ=21)

                                     tCGCATCCGGCGTTGAATGAACGCATAAAAGCAAAAAGCTCGCCGTTGCGAGCTTTTTTCCTGGGTCTGGAGTACGAGGATTCGAACCTCGGAAGGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTgg                                                                                                <  2:320707/143‑1 (MQ=18)

                                            cGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGCATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGCGCACt                                                                                         >  2:103841/1‑143 (MQ=255)

                                            cGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACt                                                                                         >  1:371506/1‑143 (MQ=255)

                                                      tgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTaa                                                                               <  2:556858/143‑1 (MQ=255)

                                                       gaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGC‑TTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGc                                                                             <  1:23166/143‑1 (MQ=255)

                                                        aaCGCAGAAAAGCAAACTGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGc                                                                             <  2:72967/143‑1 (MQ=255)

                                                             aGAAAAGCAAAACGCGCGCCGAAGCCAGCTTTGTTAATTTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCtt                                                                        <  2:472690/143‑1 (MQ=21)

                                                               aaaaGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATGCGGTGCCTTACGGCTTGGCGATACCCGAACTGGGGGCACGTACAAGGTAAGCgccgtgt                                                                      >  2:447091/1‑137 (MQ=21)

                                                                  aGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCCCGTACAAGGCATGCGTCTTGactc                                                                   >  1:499351/1‑140 (MQ=21)

                                                                      aacaGCTCGCCTAAGCGAGCTGTTTTAATGTTGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAAGTAGATTCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAtt                                                               <  2:336661/140‑1 (MQ=25)

                                                                       gaggCTCGCCGAAGCGAGCTTGTTTAAGGTGGCGGGGGGACGAGGATTCGAACCGCGGAATGCCGGAATTAGAAGCCGGTGCCTGACCGCGTGGCGATAGCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTg                                                              <  2:197832/140‑1 (MQ=255)

                                                                       aaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTCAGCGTCTTGAATAAATTg                                                              >  1:501964/1‑143 (MQ=255)

                                                                         aGCCCGCCGCGGCGAGCTTTTTTAGTGCGGCTGGGGTACGAGGATTCGAACCTCGGAGTGCCGGAATTAGAAGCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGc                                                            <  2:391643/143‑1 (MQ=21)

                                                                             cgcgGAAGCGAGCTTTTTTAATGTGGCTGGGGGACGGGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTggg                                                        <  2:149662/143‑1 (MQ=255)

                                                                                cGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCAGAATTAGAATCCGGTGACTTACCGCTTGGCGATACCCCAACTGGGGGCACTTACAAGGGAAGCGTATTGAATAAATTGGCTCGGGTa                                                     >  1:63368/1‑143 (MQ=21)

                                                                                          ttttttAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCg                                           >  1:465329/1‑143 (MQ=255)

                                                                                          ttttttAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTAAAGGGGAAGCGCTTTGAATAAATTGGCGGGGGTACggggctacg                                           >  1:468585/1‑138 (MQ=18)

                                                                                           tttttAGTGTCGCGGGGGTACGAGGATGCTGCCCTCGGAATGCCTGAAGTAGAATCCGGTGGCTGATCGCTTGTCTATACCCCACGTGGGTGCACTGACAACGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGAtttaa                                          <  2:277504/143‑4 (MQ=255)

                                                                                            tgggaaggtgGCGGGGGTACGAGGATTCGAACCTCGGAATGGCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGaa                                         <  1:480386/136‑1 (MQ=25)

                                                                                                        tGGGGTACGAGGATGCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGcc                             <  1:252938/143‑1 (MQ=255)

                                                                                                            gTACCAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGaa                         <  1:447091/143‑1 (MQ=255)

                                                                                                               cGAGGGTTCGAGCCGCGGAATGCGGGAATTAGAATCCCGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGGCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCa                      <  2:193237/143‑1 (MQ=37)

                                                                                                                          aCCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGc           <  1:192317/143‑1 (MQ=255)

                                                                                                                              cgggaggCCGGGATGAGAAAGCGGCGCCTTACAGCTTGGCGATACCCCGACGGGGTGCACGTACGAGGTAGGCGGCTTGATTAAAGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTa       <  2:30854/137‑1 (MQ=18)

                                                                                                                                   tGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCAATTAAAAGGCCAGCGAGTAGAATACGTAGGCTGAGGTACGAGGCTACGAACCTGGGCGCGCCGGAAACCGAATCCGGAGCCTAACCgag  >  2:524865/1‑141 (MQ=12)

CGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCT  >  NC_000913/696330‑696603

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