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
A2 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,457,801	A→G	Y102C (TAC→TGC)	paaF →	2,3‑dehydroadipyl‑CoA hydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,457,801	0	A	G	100.0%	139.1 / NA	39	Y102C (TAC→TGC)	paaF	2,3‑dehydroadipyl‑CoA hydratase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/22); total (17/22)

TTTTGCCGCTGGGGCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTACGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCAACGTTTA  >  NC_000913/1457670‑1457928

ttttGCCGCTGGGGCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCtt                                                                                                                          <  2:919704/139‑1 (MQ=255)

        cTGGGGCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCg                                                                                                                    <  2:935851/137‑1 (MQ=255)

        cTGGGGCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCg                                                                                                                    >  1:935851/1‑137 (MQ=255)

                gATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAAc                                                                                                          <  1:384732/139‑1 (MQ=255)

                  tctcAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTg                                                                                                        >  1:89998/1‑139 (MQ=255)

                   ctcAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTgg                                                                                                       <  2:394593/139‑1 (MQ=255)

                     cAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     <  1:338824/139‑1 (MQ=255)

                     cAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     <  2:89998/139‑1 (MQ=255)

                     cAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     <  1:412524/139‑1 (MQ=255)

                     cAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     <  1:427349/139‑1 (MQ=255)

                                  gAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGAtg                                                                                        <  2:73459/139‑1 (MQ=255)

                                      aaGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATgtggt                                                                                    <  2:105898/139‑1 (MQ=255)

                                        gATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGtggtgg                                                                                  <  2:914153/139‑1 (MQ=255)

                                         aTCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTtgtg                                                                                             >  2:538537/1‑127 (MQ=255)

                                         aTCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTtgtg                                                                                             <  1:538537/127‑1 (MQ=255)

                                                                    gTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGtt                                                      >  2:630994/1‑139 (MQ=255)

                                                                         cAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCgg                                                 >  2:440249/1‑139 (MQ=255)

                                                                                gggCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGtggtgg                                                                                  <  2:107081/99‑1 (MQ=255)

                                                                                gggCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGtggggg                                                                                  >  1:107081/1‑99 (MQ=255)

                                                                                       aTTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTgg                                                                                                       >  2:704336/1‑71 (MQ=255)

                                                                                       aTTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTgg                                                                                                       <  1:704336/71‑1 (MQ=255)

                                                                                                cTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCt                          >  1:293967/1‑139 (MQ=255)

                                                                                                cTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCt                          >  1:535783/1‑139 (MQ=255)

                                                                                                  ttAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     >  1:170398/1‑62 (MQ=255)

                                                                                                  ttAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     <  2:170398/62‑1 (MQ=255)

                                                                                                  ttAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGAt                                                                                         <  1:715827/74‑1 (MQ=255)

                                                                                                  ttAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGAt                                                                                         >  2:715827/1‑74 (MQ=255)

                                                                                                  ttAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTgg                        >  1:231185/1‑139 (MQ=255)

                                                                                                          ccACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGga                                                                          <  2:392092/81‑1 (MQ=255)

                                                                                                          ccACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGga                                                                          >  1:392092/1‑81 (MQ=255)

                                                                                                              ttATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGcat                                 <  2:534372/118‑1 (MQ=255)

                                                                                                              ttATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGcat                                 >  1:534372/1‑118 (MQ=255)

                                                                                                                 tCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCa         <  2:329697/139‑1 (MQ=255)

                                                                                                                  cGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     >  2:756906/1‑46 (MQ=255)

                                                                                                                  cGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     <  1:756906/46‑1 (MQ=255)

                                                                                                                  cGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGtttt                                                           <  2:397490/88‑1 (MQ=255)

                                                                                                                  cGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGtttt                                                           >  1:397490/1‑88 (MQ=255)

                                                                                                                       ccGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCAACGttt   >  2:115956/1‑139 (MQ=255)

                                                                                                                        cGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCAACGTTTa  <  2:231185/139‑1 (MQ=255)

TTTTGCCGCTGGGGCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTACGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCAACGTTTA  >  NC_000913/1457670‑1457928

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A