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
A0 F0 I1 R1	16	48.9	1703346	91.6%	1560264	146.2

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	97.1%	103.0 / NA	36	A1074D (GCT→GAT)	yphG	DUF4380 domain‑containing TPR repeat protein
Reads supporting (aligned to +/- strand): ref base G (0/1); new base T (17/17); total (17/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCA  >  NC_000913_3_pae_tpiA/2679381‑2679665

gggTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCgg                                                                                                                                          <  1:345713/149‑1 (MQ=255)

          taACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGcc                                                                                                                                <  1:263061/149‑1 (MQ=255)

              aacGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACATTTAATAGGGTTTAGTGAATGCGTTCATAAATAAAAGTAAGCACGTCGGTGAATAATGCCGCTCTCGGCCAATACTGATTCATCGCCGTcg                                                                                                                            >  2:499783/1‑148 (MQ=255)

               acGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCaa                                                                                                                           <  1:822357/149‑1 (MQ=255)

               acGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCaa                                                                                                                           <  1:422307/149‑1 (MQ=255)

                     tATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAgc                                                                                                                     <  1:2249/149‑1 (MQ=255)

                         ttAATTATGTTGTGATGAGCGGCAGCGCGTGCCGTTCAAATATTACAGTTAATAGGGTTTAGGGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGa                                                                                                                 <  1:391646/148‑1 (MQ=255)

                           aaTTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGc                                                                                                               >  1:649090/1‑149 (MQ=255)

                            attattTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCa                                                                                                              >  1:688588/1‑149 (MQ=255)

                                ttttGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAACATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCCATTCAGCGCGAGCAGACt                                                                                                          >  1:52671/1‑149 (MQ=255)

                                                 gcgcGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTAAAAAATAAAAGGCATCACGGTGGTAAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCACCGCGAGCAGACTCATATTGCGCAaccacc                                                                                         >  2:353033/1‑149 (MQ=255)

                                                                    tACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCACTTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGCGTCCCGCGCACGCCa                                                                      >  2:652013/1‑149 (MQ=255)

                                                                       aGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCa                                                                   >  1:303031/1‑149 (MQ=255)

                                                                             tAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAGTAATGCAGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGTGAGCAGCCCCATATTGCGCAACCCCCCCGAGTCCCCCGGACGCCACCATCGccc                                                             >  2:644978/1‑148 (MQ=255)

                                                                                 gTTTAGTGAAGTCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCAt                                                         <  2:391570/149‑1 (MQ=255)

                                                                                      gTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGc                                                    <  1:546779/149‑1 (MQ=255)

                                                                                         aaCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACCCACATTGCGCAACCTCCCCGAGCACCGCCGCCGCCACCACCCCCACCACCAGGCact                                                 >  2:402466/1‑147 (MQ=255)

                                                                                          aCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCAttt                                                <  2:688588/149‑1 (MQ=255)

                                                                                            gcgGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCAGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTACCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCAttttt                                              >  1:59062/1‑149 (MQ=255)

                                                                                               gTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCtt                                           >  2:187603/1‑149 (MQ=255)

                                                                                                 tAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTa                                         <  1:552441/149‑1 (MQ=255)

                                                                                                   aaaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAtg                                       <  1:429092/149‑1 (MQ=255)

                                                                                                        aaaaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATgctgct                                  <  1:183094/149‑1 (MQ=255)

                                                                                                           aGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATAGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgtt                               <  1:647503/149‑1 (MQ=255)

                                                                                                            ggCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAGGCCAGCATCGCCACTATCAGGCATTTTTCTTTATGCTGCtgttg                              >  1:180623/1‑149 (MQ=255)

                                                                                                                      tgagtaataagCCCCCTTTCGTCCAAGCCGGATAAATCTCCGTCAATTCAGCCCGAGCAGACTCATATTGCCCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATTCTGCTGTTGTAAATCGCCa                    <  2:620370/144‑1 (MQ=255)

                                                                                                                        gtgAATAATGTCGCTTTCGGCCAAACAGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATa                  <  1:302238/149‑1 (MQ=255)

                                                                                                                          gAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCACGAGATGACCCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAACTCGCCATACa                >  1:803349/1‑149 (MQ=255)

                                                                                                                              aatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGa            <  1:339338/149‑1 (MQ=255)

                                                                                                                               atGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGac           <  1:107326/149‑1 (MQ=255)

                                                                                                                                   cGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTGTTTATGCGGCTGTTGTAAATCGACATACAGTGacgaga       >  1:141659/1‑145 (MQ=255)

                                                                                                                                   cGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGacaaca       >  1:549268/1‑149 (MQ=255)

                                                                                                                                   cGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGacaaca       >  1:549213/1‑149 (MQ=255)

                                                                                                                                    gCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTAATAATGCGCAAGCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTTTGAATCGCCATACGGCGAcgacaa      >  2:353643/1‑149 (MQ=255)

                                                                                                                                    ccTTTCGGCCACTCCTGATTAATCGCCTTCAATTCAACGCGAGCAGCCTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTGTATGCTGCTGTTGTAAATCGCCATACAGCGAcaacaa      <  1:373307/148‑1 (MQ=255)

                                                                                                                                        tCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCa  <  1:187603/149‑1 (MQ=255)

GGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCA  >  NC_000913_3_pae_tpiA/2679381‑2679665

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