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 F104 I1 R1	25	31.6	1325236	90.2%	1195362	142.4

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	93.8%	74.6 / NA	32	noncoding (35/75 nt)	glnX	tRNA‑Gln
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (11/19); minor base G (0/2); total (11/21)
Fisher's exact test for biased strand distribution p-value = 5.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGG  >  NC_000913/696335‑696606

cATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATcc                                                                                                                                   >  1:48148/1‑143 (MQ=255)

     gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGAATCGAACCTCGGAATGCAGGAATTAAAATCAGGTGc                                                                                                                              >  2:40398/1‑143 (MQ=255)

     gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATAGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGc                                                                                                                              <  1:133229/143‑1 (MQ=255)

             aGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGc                                                                                                                      >  2:550032/1‑143 (MQ=255)

                aTAAGACGGGTTAAAATCGCAGTCGAGATTGAGTGAACGCAGAAAAGCAAAAAGGTCGCCGAAGCGAGCGTTGTTAAGGTGGCTGGGGTACGGGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTg                                                                                                                   <  2:501430/143‑1 (MQ=21)

                  aaGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGGATTAGAATCCGGTGCCTTACCGCTTGGc                                                                                                                 <  1:287346/143‑1 (MQ=255)

                  aaGACGTGTCAACATCGCATGCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTTGGAATGCCGTAATTAGAATCCGGTGCCTTACCGCTTGGc                                                                                                                 <  1:95209/143‑1 (MQ=255)

                       gtgtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAc                                                                                                            <  1:288631/143‑1 (MQ=255)

                          ttatcATCGCAGTGGACATGGAATGAACGCAGAAAAGCAAAAAGCGCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAcccc                                                                                                         <  2:580755/139‑1 (MQ=21)

                                tCGCATGCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTgg                                                                                                   <  2:150076/143‑1 (MQ=255)

                                     ttCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCa                                                                                              <  1:263989/143‑1 (MQ=255)

                                         gtcttgattgaTTGCAGAAATGGTAAGAGCTCGCCGAAGCGAGCTTTTGTAATGTGGCGGGGGTACGAGGAGTCGAACCTCGTAATGCCGGACTTAGAATCCGGTGCCTTACTGCGTGGCGATACCCCAACTTGGTGCACTTa                                                                                          <  2:70684/140‑1 (MQ=255)

                                           aTTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGGACTTACa                                                                                        >  2:478563/1‑143 (MQ=255)

                                                    aCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCg                                                                               >  1:498149/1‑143 (MQ=255)

                                                       cAGAAAAGCAAAACGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCt                                                                            <  1:235018/143‑1 (MQ=255)

                                                       cAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGCAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCt                                                                            <  1:288097/143‑1 (MQ=255)

                                                          aaaaGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTAGCTGGGGTACGAGGATTCGAACCTCGAAATGCCGAAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTATAAGGTAATCGACTTgc                                                                         >  1:433294/1‑142 (MQ=25)

                                                                       tCGCCGAATCGGGGTTTTTTAATTTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGGATTAGGAGCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTgg                                                            <  2:659446/143‑1 (MQ=21)

                                                                       tCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTgg                                                            <  1:405504/143‑1 (MQ=255)

                                                                               gCGAGCTGTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAg                                                    <  2:254912/143‑1 (MQ=255)

                                                                                       ctggaaTGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGaa                                            <  1:18824/139‑1 (MQ=255)

                                                                                            aTGGGGTTGGGGCACGAGGATTCGAACCTCGGAATGCCGGAATGAGACTCCGGTGCCTTACCGCGTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCg                                       <  1:249408/143‑1 (MQ=25)

                                                                                                  cTGGGGTACGAGGATTCGAACGTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGTGGTACGAGGATTCGAACCTCGAAATGc                                 <  1:639373/143‑1 (MQ=255)

                                                                                                  cTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGc                                 <  2:498149/143‑1 (MQ=255)

                                                                                                   tGGGGGACGAGGATTCGAACCGCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGcc                                <  1:635769/143‑1 (MQ=255)

                                                                                                        tACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACACGGGAAGCGCCNTGAACAAATCGGCTGAGGAACGAGGCTGCGCAGCGCGGAAAGCCGGaaa                           >  1:446415/1‑142 (MQ=18)

                                                                                                            aGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGACTGCCggccccgga                       >  1:271331/1‑136 (MQ=255)

                                                                                                            aGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGa                       >  1:498846/1‑143 (MQ=255)

                                                                                                                    aaCCTCGGAATGCCGGAATGAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTg               <  1:184838/143‑1 (MQ=255)

                                                                                                                         cGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCggagaatta          >  1:145393/1‑136 (MQ=255)

                                                                                                                                ccGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTACGCGTCTTGGATAAATTGGCTGGGGTACGAAGCTAAGAACCTCGGAATGCCGCAATCAGATACGTGTGCCTTTCCGCTTg   >  1:301718/1‑143 (MQ=25)

                                                                                                                                 cGGAATTACAATCCGGTGCCTTACCCCTCGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTTGCTGGGGTACGAGGACTCGAACCTCGTAATGCCGGAATCATAATCCGGTGCCTTACCGCTTgg  <  1:631378/143‑1 (MQ=25)

CATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGG  >  NC_000913/696335‑696606

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