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 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,656,658	G→A	A159T (GCC→ACC)	speG →	spermidine N(1)‑acetyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,656,658	0	G	A	100.0%	142.6 / NA	42	A159T (GCC→ACC)	speG	spermidine N(1)‑acetyltransferase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/22); total (20/22)

TCTCAATCTCTATAAGCTGTATCTGATCGTTGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATGCCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAATCGATCGTATTTTTGA  >  NC_000913/1656525‑1656772

tctcAATCTCTATAAGCTGTATCTGATCGTTGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCAtt                                                                                                               >  1:577006/1‑139 (MQ=255)

    aaTCTCTATAAGCTGTATCTGATCGTTGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCa                                                                                                           <  1:263704/139‑1 (MQ=255)

                     tCTGATCGTTGATAAAGAGAATGACAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCAt                                                                                          <  2:367218/139‑1 (MQ=255)

                         aTCGTTGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCAt                                                                                          <  2:452819/135‑1 (MQ=255)

                         aTCGTTGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCAt                                                                                          >  1:452819/1‑135 (MQ=255)

                             ttGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGTAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCAtt                                                                                                               <  1:158438/110‑1 (MQ=255)

                             ttGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATCTCGTAATACCAtt                                                                                                               <  1:437739/110‑1 (MQ=255)

                             ttGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCAtt                                                                                                               >  2:158438/1‑110 (MQ=255)

                             ttGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCAtt                                                                                                               >  2:437739/1‑110 (MQ=255)

                             ttGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCt                                                                                  >  2:53693/1‑139 (MQ=255)

                             ttGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCt                                                                                  >  2:122898/1‑139 (MQ=255)

                                       gaATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTcc                                                                                               <  1:473957/116‑1 (MQ=255)

                                       gaATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTcc                                                                                               >  2:473957/1‑116 (MQ=255)

                                        aaTGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCa                                                                                                                 >  1:189095/1‑97 (MQ=255)

                                        aaTGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCa                                                                                                                 <  2:189095/97‑1 (MQ=255)

                                        aaTGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGc                                                                                                            >  1:587826/1‑102 (MQ=255)

                                        aaTGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGc                                                                                                            <  2:587826/102‑1 (MQ=255)

                                        aaTGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCAt                                                                                                          <  1:38056/104‑1 (MQ=255)

                                        aaTGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCAt                                                                                                          >  2:38056/1‑104 (MQ=255)

                                        aaTGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCAt                                                                                          >  2:37220/1‑120 (MQ=255)

                                        aaTGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCAt                                                                                          <  1:37220/120‑1 (MQ=255)

                                                aGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCAt                                                                                                          >  2:174230/1‑96 (MQ=255)

                                                aGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCAt                                                                                                          <  1:174230/96‑1 (MQ=255)

                                                  cGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGc                                                                                                            <  2:448933/92‑1 (MQ=255)

                                                  cGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGc                                                                                                            >  1:448933/1‑92 (MQ=255)

                                                                    aGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCg                                                                                                             <  2:558107/73‑1 (MQ=255)

                                                                    aGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCg                                                                                                             >  1:558107/1‑73 (MQ=255)

                                                                       ttGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGAc                                        <  2:577006/139‑1 (MQ=255)

                                                                               tCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATTTGTATATTCCAGCATCAGTATCTGGCa                                                                              <  1:392698/93‑1 (MQ=255)

                                                                               tCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTggaa                                                                              >  2:392698/1‑91 (MQ=255)

                                                                                                   gCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCg                                                                                                             <  2:368878/42‑1 (MQ=255)

                                                                                                   gCACGAGTTCTTTATTAATGGTCAATATCGTAATACCATTCg                                                                                                             >  1:368878/1‑42 (MQ=255)

                                                                                                            cTTTATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAATCGATCGTATTTTTg   >  2:355787/1‑139 (MQ=255)

                                                                                                             tttATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAATCGATCGTATTTTTGa  <  2:571966/139‑1 (MQ=255)

                                                                                                             tttATTAATGGTCAATATCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAATCGATCGTATTTTTGa  <  1:122898/139‑1 (MQ=255)

                                                                                                             tttATTAATGGTCAATATCGTAATACCACTCGCATGTGTATATTCCACCATCGGTGTCGGGCACAGCACAAAACACCGGGTCAGACGCTCCTGCAGCCGTCCGCGACATAGCATTAATAATAATCGATGGCTTTTTTGa  <  1:431722/139‑1 (MQ=255)

                                                                                                                           atatCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGa                                                        <  1:654920/71‑1 (MQ=255)

                                                                                                                           atatCGTAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGa                                                        >  2:654920/1‑71 (MQ=255)

                                                                                                                                 tAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAatcgatc            >  1:591463/1‑109 (MQ=255)

                                                                                                                                 tAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAatcgatc            <  2:591463/109‑1 (MQ=255)

                                                                                                                                 tAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAATCGATCGTATTTTTGa  >  1:171214/1‑119 (MQ=255)

                                                                                                                                 tAATACCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAATCGATCGTATTTTTGa  <  2:171214/119‑1 (MQ=255)

TCTCAATCTCTATAAGCTGTATCTGATCGTTGATAAAGAGAATGAAAAAGCGATTCACATTTACCGCAAGCTTGGCTTTTCGGTTGAAGGTGAATTGATGCACGAGTTCTTTATTAATGGTCAATATCGTAATGCCATTCGCATGTGTATATTCCAGCATCAGTATCTGGCAGAGCACAAAACACCGGGTCAGACTCTCCTGAAGCCGACCGCACAATAGCATTAATAATAATCGATCGTATTTTTGA  >  NC_000913/1656525‑1656772

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A