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
A7 F1 I1 R1	83	73.5	3575638	92.3%	3300313	107.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,392,496	C→T	noncoding (25/76 nt)	glyX →	tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,392,496	0	C	T	98.0%	163.6 / NA	51	noncoding (25/76 nt)	glyX	tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (25/25); total (25/26)
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

TAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCG  >  NC_000913/4392367‑4392625

tAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTg                                                                                                                          <  1:1354119/139‑1 (MQ=255)

tAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTg                                                                                                                          >  2:1354119/1‑139 (MQ=255)

  gCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGcc                                                                                                                        <  1:22583/139‑1 (MQ=255)

             agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTGGGTAGAGTACGACCTTGCCAAGGTCGGGGt                                                                                                             >  1:1168833/1‑139 (MQ=255)

                gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTcgc                                                                                                          >  2:1149115/1‑139 (MQ=255)

                 cACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTcgcg                                                                                                         <  2:331021/139‑1 (MQ=255)

                     aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACC‑TGCCAAGGTCGGGGTCGCGAGTTc                                                                                                    >  2:1761888/1‑139 (MQ=255)

                         tGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAg                                                                                                 >  1:331021/1‑139 (MQ=255)

                                gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGtt                                                                                          >  2:1106591/1‑139 (MQ=255)

                                gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGtt                                                                                          >  2:775322/1‑139 (MQ=255)

                                    gggTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTccc                                                                                      >  1:1705230/1‑139 (MQ=255)

                                     ggTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCg                                                                                     >  1:739192/1‑139 (MQ=255)

                                              ttCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACC‑TGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAtt                                                                           <  1:1761888/139‑1 (MQ=255)

                                                       cGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                                   <  1:1106591/139‑1 (MQ=255)

                                                         tttCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                                 >  1:353891/1‑139 (MQ=255)

                                                           tCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                               <  2:924994/139‑1 (MQ=255)

                                                           tCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                               <  2:353891/139‑1 (MQ=255)

                                                                       aTTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                                   <  1:1149115/139‑1 (MQ=255)

                                                                          tGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccacc                                                <  1:18609/139‑1 (MQ=255)

                                                                           gAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCgggg                                                                                                              >  1:952597/1‑76 (MQ=255)

                                                                           gAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCgggg                                                                                                              <  2:952597/76‑1 (MQ=255)

                                                                              aaGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                            <  2:739192/139‑1 (MQ=255)

                                                                                 tgctgcAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGt                                                                                                                   <  1:508503/65‑1 (MQ=255)

                                                                                 tgctgcAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGt                                                                                                                   >  2:508503/1‑65 (MQ=255)

                                                                                      cAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                                    <  2:963577/139‑1 (MQ=255)

                                                                                      cAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                                    >  1:573770/1‑139 (MQ=255)

                                                                                           cacaGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                                   >  2:875238/1‑103 (MQ=255)

                                                                                           cacaGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                                   <  1:875238/103‑1 (MQ=255)

                                                                                             caGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGt                             <  2:573770/139‑1 (MQ=255)

                                                                                                aaccaccAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTgg                          <  1:1341422/134‑1 (MQ=255)

                                                                                                     ccAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                                   <  1:1307569/93‑1 (MQ=255)

                                                                                                     ccAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                                   >  2:1307569/1‑93 (MQ=255)

                                                                                                     ccAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTagag                     >  1:158492/1‑139 (MQ=255)

                                                                                                     ccAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGCCACAGACTACCCAAGCGGGAATAGCTCAGTTGGTagag                     >  1:862066/1‑139 (MQ=255)

                                                                                                     ccAAGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGCGATGTAAGGCCCACACCACCCAGGCGGGAAAAGGTCAGTTGGTagag                     >  1:356187/1‑139 (MQ=14)

                                                                                                     ccAAGCGGGAATAGCTCAGTTGGT‑GAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGc                    >  2:216560/1‑139 (MQ=255)

                                                                                                       aaGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCa                   <  2:158492/139‑1 (MQ=255)

                                                                                                       aaGCGGGAATAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCa                   <  2:1705230/139‑1 (MQ=255)

                                                                                                          cGGGAATAGCTCAGTTGGTAGAGTACAACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa                >  2:328097/1‑139 (MQ=255)

                                                                                                           gggAATAGCTCAGTTGGTAGAGTACAACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc               <  1:328097/139‑1 (MQ=255)

                                                                                                              aaTAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTa                                                              <  1:640796/89‑1 (MQ=255)

                                                                                                              aaTAGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTa                                                              >  2:640796/1‑89 (MQ=255)

                                                                                                                 aGCTCAGTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGcc         <  2:900736/139‑1 (MQ=255)

                                                                                                                 aGCTCAGTTGGCAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTGCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGcc         <  2:1168833/139‑1 (MQ=255)

                                                                                                                       gTTGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTc   >  1:900736/1‑139 (MQ=255)

                                                                                                                        ttGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                               <  1:885516/78‑1 (MQ=255)

                                                                                                                        ttGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                               >  2:885516/1‑78 (MQ=255)

                                                                                                                        ttGGTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCg  >  2:1055602/1‑139 (MQ=255)

                                                                                                                           gTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                                     >  2:517760/1‑69 (MQ=14)

                                                                                                                           gTAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                                     <  1:517760/69‑1 (MQ=14)

                                                                                                                            tAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                                   >  1:1534615/1‑70 (MQ=255)

                                                                                                                            tAGAGTACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                                   <  2:1534615/70‑1 (MQ=255)

TAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAGTGCTGCAAAGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCG  >  NC_000913/4392367‑4392625

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A