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
A3 F71 I1 R1	22	42.5	1502764	94.6%	1421614	143.6

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%	99.9 / NA	34	A1074D (GCT→GAT)	yphG	DUF4380 domain‑containing TPR repeat protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (12/22); total (12/22)

TTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAG  >  NC_000913_3_hsa_tpiA/2679387‑2679662

ttattaACAACGGCTTATTTTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAAt                                                                                                                                  <  1:127910/149‑1 (MQ=255)

   ttaACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGAGCGGCTCAAATATTACAGTTAATAGGGGTTAGTGAACGCCGTTAAAAATAAACGGCATCCCGGTCGTGACTAATACCGCTTCAGGCCACTCCGCATTACTCGc                                                                                                                               >  2:532370/1‑149 (MQ=255)

    taACAACGGCCTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGcc                                                                                                                              <  1:163489/149‑1 (MQ=255)

        aacGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTcc                                                                                                                          >  2:291661/1‑148 (MQ=255)

          cGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAAt                                                                                                                                  >  2:405293/1‑139 (MQ=255)

          cGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAAt                                                                                                                                  <  1:405293/139‑1 (MQ=255)

                aTTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAgcg                                                                                                                  <  2:188495/149‑1 (MQ=255)

                      attattTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGGGGTGAATAATGCCGCTTTCGGCCAATCCGGCTTAATCGCCGTCAATTCAGCGCGAGCa                                                                                                            >  1:218236/1‑149 (MQ=255)

                           tttGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATTGCCGTCAATTCAGCGCGAGCAGACTc                                                                                                       >  2:100243/1‑149 (MQ=255)

                           tttGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTc                                                                                                       <  1:521147/149‑1 (MQ=255)

                                gatgaGCGGCAGCGCGTGCCGCTCAATTATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGGATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATAtt                                                                                                  <  1:533450/149‑1 (MQ=255)

                                    aGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTg‑cgc                                                                                             <  1:318413/149‑1 (MQ=255)

                                            gcgctGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGa                                                                                                          <  2:48837/125‑1 (MQ=255)

                                            gcgctGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGa                                                                                                          >  1:48837/5‑129 (MQ=255)

                                               gggCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCGTCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGa                                                                                  <  1:70159/147‑1 (MQ=255)

                                                      tCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCcgc                                                                           >  2:681839/1‑149 (MQ=255)

                                                              tACAGTTAATAGGGTTTAGTGAAAGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCa                                                                   <  2:519845/149‑1 (MQ=255)

                                                                   ttAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCCAGCAGACTCATATTG‑CGCAACCTCCCCGAGCCCCGCGGACGCCCGCATc                                                              >  2:18934/1‑149 (MQ=255)

                                                                      aTAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGcc                                                           <  1:681839/149‑1 (MQ=255)

                                                                         gggTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGccacc                                                        <  1:204162/149‑1 (MQ=255)

                                                                                gTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGc                                                 >  1:187600/1‑149 (MQ=255)

                                                                                       cgGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTc                                          <  1:240079/149‑1 (MQ=255)

                                                                                          ttAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCttt                                       >  1:506278/1‑149 (MQ=255)

                                                                                            aaaaaTAAAAGGCCGCACGGTGGTGAATAATGCCGCTTTCGGACAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAt                                     <  2:218236/149‑1 (MQ=255)

                                                                                              aaaTAAAAGGCATCACGGTGGTGAATAATGCAGCTTTCGACCAATCCGGATTAATCGCCGTCAATTCAGCGCGAACAGACTAAAATTG‑CGCAACCTCCCCGAATCCCGCGGACGCCAGCATAGCCACCATCCGGCATTTTTCGTTAtgc                                   >  2:356036/1‑149 (MQ=255)

                                                                                                  aaaaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATgctgct                               <  2:237981/149‑1 (MQ=255)

                                                                                                     aGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgtt                            <  2:52143/149‑1 (MQ=255)

                                                                                                             cGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCg                    <  2:393888/149‑1 (MQ=255)

                                                                                                                      ataatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGc           <  2:187600/149‑1 (MQ=255)

                                                                                                                           gCCTCTTTCGGCCAATCCGGATTAATCGCCGTAAATTGAGCGAGCG‑AAACCAATTTTGTCGCAGCCGCCCCGAGTCCCGGGGACGCGAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGacaa      <  2:535373/149‑1 (MQ=255)

                                                                                                                           gCCGCTTTCGGCCAATCCGGATAAATCGCCCGCAAGGCAGCGCACGCAGTCTCGTATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGacaa      <  1:100243/149‑1 (MQ=255)

                                                                                                                              gCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGCACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGAcaacaa   <  1:481018/149‑1 (MQ=255)

                                                                                                                               cTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCGCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAg  <  2:460910/149‑1 (MQ=255)

                                                                                                                               cTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACATCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAg  >  2:177347/1‑149 (MQ=255)

TTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTG‑CGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAG  >  NC_000913_3_hsa_tpiA/2679387‑2679662

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