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
A4 F4 I1 R1	17	32.4	1141670	89.0%	1016086	148.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	2,679,525	G→T	A1074D (GCT→GAT)	yphG ←	DUF4380 domain‑containing TPR repeat protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_tpiA	2,679,525	0	G	T	100.0%	79.9 / NA	30	A1074D (GCT→GAT)	yphG	DUF4380 domain‑containing TPR repeat protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (14/16); total (14/16)

ATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCA  >  NC_000913_3_hsa_tpiA/2679389‑2679665

attaACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCg                                                                                                                                  >  1:70716/1‑149 (MQ=255)

 gtgacaacGGCTTATTCTAATTTTGTTGTGATGAGCGGCTGCGCGTGGCGTTTAAATATTATCGTTAATAGGGTTTAGTGATCGCGGTTAAAAATAAAAGGCCTCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGc                                                                                                                                 <  2:535115/146‑1 (MQ=255)

  taACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGcc                                                                                                                                <  1:473585/149‑1 (MQ=255)

            ttATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTAAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAg                                                                                                                      >  2:523215/1‑149 (MQ=255)

                             tgatgtGCGGCAGCGCTTCACGCGTAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCatat                                                                                                     <  2:397963/149‑1 (MQ=255)

                                tgaGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGCACGCGGTTAAAAATAAAAGGCATAACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTgc                                                                                                  <  1:118758/149‑1 (MQ=255)

                                tgaGCCGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGACCGCGGTTAAAAATAAAAGGCATCGCGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTgc                                                                                                  <  1:16148/149‑1 (MQ=255)

                                      gCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAAcc                                                                                            >  1:306115/1‑149 (MQ=255)

                                                       aaTATTACAGTTAATAGGGGTTAGTGAACGCGGTGAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGa                                                                           <  1:1339/149‑1 (MQ=255)

                                                              cAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGc                                                                    >  1:518606/1‑149 (MQ=255)

                                                               aGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATACGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACCCCAGCa                                                                   >  1:126230/1‑149 (MQ=255)

                                                                          tttAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACACATATTGCGCAACCTCCCCGAGGCCCGCGGACGCCAGCATCGCCACCATc                                                        >  1:290837/1‑149 (MQ=255)

                                                                           ttAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCa                                                       <  1:112435/149‑1 (MQ=255)

                                                                           ttAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAAGAATGCCGCTTTCGGCACATCAGGAGTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCa                                                       <  1:271593/149‑1 (MQ=255)

                                                                             aGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAgg                                                     <  1:30477/149‑1 (MQ=255)

                                                                                 aaCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAGTTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAAGCCACCCTATCCCCCATCAAGCAtt                                                 >  2:43757/1‑149 (MQ=255)

                                                                                 aaCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCACATTAGTCAACCTCCCACAGACCCCCGGACGCCAGCATCGCCACCATCAGGCAtt                                                 >  1:76008/1‑149 (MQ=255)

                                                                                  aCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATCCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCAttt                                                <  1:361456/149‑1 (MQ=255)

                                                                                    gaggTTAAAAATTAAAGGCATTTCGGTGGTGAATAATGCCGCTTTCGGGCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCAAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCAttttt                                              <  2:337874/147‑1 (MQ=255)

                                                                                           aaaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCCCCATCAGGCATTTTTCTTTCtg                                       >  1:428868/1‑149 (MQ=255)

                                                                                                   aGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgtt                               <  1:389855/149‑1 (MQ=255)

                                                                                                         cACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGGTTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAAt                         <  2:199416/149‑1 (MQ=255)

                                                                                                          aCGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGCCTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCCGGCATTTTTCTTTATGCTGCGCTTGTACATc                        >  2:159388/1‑149 (MQ=255)

                                                                                                            ggtggtGGATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACGATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGc                      >  1:527770/1‑149 (MQ=255)

                                                                                                                gtgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATa                  >  1:547104/1‑149 (MQ=255)

                                                                                                                     taatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCGATACAGCg             >  1:505812/1‑149 (MQ=255)

                                                                                                                             cTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAGGCTGCGGTTGTAAATCGCCATACAGCGACAGCAAg     >  1:533932/1‑149 (MQ=255)

                                                                                                                              tttCCGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGt    <  1:41314/149‑1 (MQ=255)

                                                                                                                                tctgCCAATGCGGTTTAATCGTCGTCAATTCAGCGCGAGTAGAGTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATTCTACTGTTGTAATTCTCCATACAGCGACGACAAGTCa  <  2:502840/146‑1 (MQ=255)

                                                                                                                                tCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCa  <  1:324488/149‑1 (MQ=255)

ATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCA  >  NC_000913_3_hsa_tpiA/2679389‑2679665

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