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
A7 F28 I1 R1	172	67.8	2301510	98.9%	2276193	138.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,781,150	T→C	intergenic (+133/‑65)	lldD → / → trmL	L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,781,150	0	T	C	100.0%	126.4 / NA	37	intergenic (+133/‑65)	lldD/trmL	L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (21/16); total (21/16)

TGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCTTTGCGCTA  >  NC_000913/3781023‑3781284

tGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAgg                                                                                                                            >  2:1139351/1‑140 (MQ=255)

                       tcCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCAc                                                                                                                      >  2:577099/1‑123 (MQ=255)

                       tcCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCAc                                                                                                                      <  1:577099/123‑1 (MQ=255)

                       tcCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg                                                                                                     >  2:666589/1‑140 (MQ=255)

                                  gagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGccc                                                                                          <  2:1067224/140‑1 (MQ=255)

                                   agGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGcccc                                                                                         <  1:319111/140‑1 (MQ=255)

                                   agGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGcccc                                                                                         <  1:460408/140‑1 (MQ=255)

                                     gggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCg                                                                                       >  1:417123/1‑140 (MQ=255)

                                       gACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCa                                                                                     >  2:877451/1‑140 (MQ=255)

                                               ggCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAgggg                                                                             <  1:877451/140‑1 (MQ=255)

                                                           aCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaa                                                                 >  1:693656/1‑140 (MQ=255)

                                                            cTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa                                                                <  1:1000901/140‑1 (MQ=255)

                                                                cTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCt                                                                   <  1:127800/133‑1 (MQ=255)

                                                                cTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCt                                                                   >  2:127800/1‑133 (MQ=255)

                                                                cTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATc                                                            >  1:1094091/1‑140 (MQ=255)

                                                                cTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATc                                                            >  1:552012/1‑140 (MQ=255)

                                                                 tCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCg                                                           <  2:1094091/140‑1 (MQ=255)

                                                                                    cACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAAcc                                              >  1:400235/1‑134 (MQ=255)

                                                                                    cACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAAcc                                              <  2:400235/134‑1 (MQ=255)

                                                                                         tttttttCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGc                                   >  1:1148525/1‑140 (MQ=255)

                                                                                          ttttttCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGcc                                  <  2:693656/140‑1 (MQ=255)

                                                                                              ttCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAAt                              <  1:1139351/140‑1 (MQ=255)

                                                                                                   ccTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGcc                                  >  1:466808/1‑131 (MQ=255)

                                                                                                   ccTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGcc                                  <  2:466808/131‑1 (MQ=255)

                                                                                                   ccTCGCCCCTCCGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTgg                         <  2:876721/140‑1 (MQ=255)

                                                                                                             ccGGGGAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACatcatc               >  1:955194/1‑140 (MQ=255)

                                                                                                                gggAGAGGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGt            >  2:234026/1‑140 (MQ=255)

                                                                                                                   agagGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCtt         >  1:901171/1‑140 (MQ=255)

                                                                                                                     agGGCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCTTTg       <  1:234026/140‑1 (MQ=255)

                                                                                                                      gggCCAGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAAcatc                  >  1:442830/1‑128 (MQ=255)

                                                                                                                      gggCCAGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAAcatc                  <  2:442830/128‑1 (MQ=255)

                                                                                                                       ggCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCTTTgcg     >  2:972474/1‑140 (MQ=255)

                                                                                                                       ggCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCTTTgcg     >  1:909002/1‑140 (MQ=255)

                                                                                                                       ggCCGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCTTTgcg     >  1:762056/1‑140 (MQ=255)

                                                                                                                          cGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCtt         <  1:117000/133‑1 (MQ=255)

                                                                                                                          cGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCtt         >  2:117000/1‑133 (MQ=255)

                                                                                                                          cGGGGCGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCTTTGCGCTa  >  1:511802/1‑140 (MQ=255)

TGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCCGCCAAATACTGGCAACATCATCCGTCTTTGCGCTA  >  NC_000913/3781023‑3781284

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A