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
A15 F3 I1 R1	17	41.7	1441332	93.3%	1344762	144.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_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_pae_tpiA	2,679,525	0	G	T	100.0%	95.3 / NA	33	A1074D (GCT→GAT)	yphG	DUF4380 domain‑containing TPR repeat protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (18/15); total (18/15)

GGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTC  >  NC_000913_3_pae_tpiA/2679381‑2679664

gggTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAATTATTTCTGCGTGGTGAATAATGCCGCTTTCGGCCAATCCgg                                                                                                                                         <  1:537149/149‑1 (MQ=255)

 ggTTTTTATTAACAACGGCTTATGTTAATTAGTTTGGGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGa                                                                                                                                        <  2:574161/149‑1 (MQ=255)

   tttttATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTAAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCACTCCGGAtt                                                                                                                                      >  2:332126/1‑149 (MQ=255)

              aacGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTACCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCa                                                                                                                           >  2:42054/1‑149 (MQ=255)

               acGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTCATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGAATTAATCGCCGTCaa                                                                                                                          >  2:676893/1‑149 (MQ=255)

                    ttATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTGAAACATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGTCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAg                                                                                                                     <  1:324317/149‑1 (MQ=255)

                      aTTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGCAGGAGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGCCAAATCCGGCTTGATCCCCGTCAtttaatcg                                                                                                                   >  2:20653/1‑144 (MQ=255)

                         cTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGACGTAAGTTCTGcgcgt                                                                                                                >  1:670143/1‑148 (MQ=255)

                                       atgaGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTg                                                                                                  <  1:3668/149‑1 (MQ=255)

                                         gaGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTgcg                                                                                                >  2:462356/1‑149 (MQ=255)

                                           gCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCa                                                                                              >  1:185648/1‑149 (MQ=255)

                                                     gTGCAGGTCAAATATTAATGTTAATAGGGTTTAGCTATCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGTTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCGCCACGa                                                                                    <  2:613079/149‑1 (MQ=255)

                                                          gCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc                                                                               <  1:645210/149‑1 (MQ=255)

                                                            tCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCcgc                                                                             >  1:391472/1‑149 (MQ=255)

                                                              aaaTATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCgg                                                                           >  1:144937/1‑149 (MQ=255)

                                                              aaaTATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCgg                                                                           >  2:377686/1‑149 (MQ=255)

                                                               aaTATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGCGTCACGCggg                                                                          >  1:290434/1‑148 (MQ=255)

                                                                      cAGTTAATAGGGTTTAGTGAACGCGGTTAAAACTAAAAGGCATCCCGGTGGTGAATAATGCCGCTTTCGGCCAATCCTGCTTAATCGCCGTCAATCCAGCGCGAGCAGGCTCATATTGCGCACTCTCCACGAGTCCATCGCACGcccac                                                                   >  2:298376/1‑146 (MQ=255)

                                                                                               gTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCtt                                          <  1:462356/149‑1 (MQ=255)

                                                                                                    aaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATc                                                                >  2:317372/1‑122 (MQ=255)

                                                                                                    aaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATc                                                                <  1:317372/122‑1 (MQ=255)

                                                                                                    aaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAtgc                                     >  1:259651/1‑149 (MQ=255)

                                                                                                          aaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgt                               >  1:579635/1‑149 (MQ=255)

                                                                                                             gCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgttgt                            <  1:291829/149‑1 (MQ=255)

                                                                                                             gCATCACGGTGGTGAATAAGGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGCCGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgttgt                            >  2:270639/1‑149 (MQ=255)

                                                                                                                    ggtggtGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGc                     >  1:344551/1‑149 (MQ=255)

                                                                                                                            ataatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGc             <  1:42054/149‑1 (MQ=255)

                                                                                                                            ataatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGc             <  2:391472/149‑1 (MQ=255)

                                                                                                                            ataagGCCGCTTTCAGCCAATGCGGATTAATCGCCGTCAATTTAGCGCGAGCAGACTCATATTGCGCATCCTTCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGc             <  2:708669/149‑1 (MQ=255)

                                                                                                                               atGCCGCTTTCGGCCAATCCGGACTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGac          <  2:670143/149‑1 (MQ=255)

                                                                                                                                  ccGCTTTCGGCCAATCCGGATTAGTCGCCGTCAATTCCGCGGGGGGAGACTCTTATTGCGAAACCTCCCCGAGTCCCGCGGACGCCAGCGTGGCTGCTATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATGGCCATGCAGCGacaac       <  2:445245/149‑1 (MQ=255)

                                                                                                                                      tttCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCAGCTGTCTCTTGTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGt   >  1:565050/1‑149 (MQ=255)

                                                                                                                                       tgcGGCCAATGCGGATTAATCGCCGTGAATTCGGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTTCCGCGGACGCCAGCATCGCCACCATGAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGAGGCAACAAATc  <  2:124787/147‑1 (MQ=255)

GGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTC  >  NC_000913_3_pae_tpiA/2679381‑2679664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A