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
A6 F1 I1 R1	750	51.0	2595496	93.6%	2429384	106.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,416,763	2 bp→TC	coding (2017‑2018/2145 nt)	pta →	phosphate acetyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,416,763	0	C	T	100.0%	118.3 / NA	37	L673S (CTG→TCG)	pta	phosphate acetyltransferase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (17/20); total (17/20)
*	NC_000913	2,416,764	0	T	C	100.0%	131.7 / NA	37	L673S (CTG→TCG)	pta	phosphate acetyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/20); total (17/20)

CTGCGGTAATGGCTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACCTGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGAT  >  NC_000913/2416632‑2416869

||

cTGCGGTAATGGCTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGAtctc                                                                                                     >  2:771719/1‑139 (MQ=255)

   cGGTAATGGCTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCAt                                                                                                  <  1:1023124/139‑1 (MQ=255)

           gCTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGa                                                                                          <  2:158797/139‑1 (MQ=255)

             tGACGTCGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGAtg                                                                                        >  2:994294/1‑139 (MQ=255)

                cGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCg                                                                                           <  2:520256/133‑1 (MQ=255)

                cGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCg                                                                                           >  1:520256/1‑133 (MQ=255)

                 gTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGa                                                                                          >  1:1257105/1‑133 (MQ=255)

                 gTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGa                                                                                          <  2:1257105/133‑1 (MQ=255)

                                           tcCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGAc                                                          <  1:43835/139‑1 (MQ=255)

                                                   cAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCg                                                  >  2:42198/1‑139 (MQ=255)

                                                   cAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCg                                                  <  2:210079/139‑1 (MQ=255)

                                                     ggTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGAtg                                                                                        <  2:1240092/99‑1 (MQ=255)

                                                     ggTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGAtg                                                                                        >  1:1240092/1‑99 (MQ=255)

                                                     ggTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTg                                                >  1:1032748/1‑139 (MQ=255)

                                                          cgcTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACACAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGTAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCa                                           <  2:800458/139‑1 (MQ=255)

                                                          cgcTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCa                                           >  2:536652/1‑139 (MQ=255)

                                                                  tgtTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGa                                   >  2:384941/1‑139 (MQ=255)

                                                                       aTCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGata                              <  2:978806/139‑1 (MQ=255)

                                                                         cTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATc                            <  1:536652/139‑1 (MQ=255)

                                                                            cccGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTg                                        <  1:389065/124‑1 (MQ=255)

                                                                            cccGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTg                                        >  2:389065/1‑124 (MQ=255)

                                                                              cGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTa                       <  2:1032748/139‑1 (MQ=255)

                                                                                      aaCACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATcg               >  2:823371/1‑139 (MQ=255)

                                                                                          ccGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCt           <  1:42198/139‑1 (MQ=255)

                                                                                            ggTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGa         <  1:771719/139‑1 (MQ=255)

                                                                                             gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGAt                                                                                         >  2:1218052/1‑58 (MQ=255)

                                                                                             gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGAt                                                                                         <  1:1218052/58‑1 (MQ=255)

                                                                                             gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGata                              >  2:318098/1‑117 (MQ=255)

                                                                                             gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGata                              <  1:318098/117‑1 (MQ=255)

                                                                                             gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATc                            <  2:842241/119‑1 (MQ=255)

                                                                                             gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATc                            >  1:842241/1‑119 (MQ=255)

                                                                                             gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGAc        >  2:728273/1‑139 (MQ=255)

                                                                                                   ccaccTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGAt  <  1:994294/139‑1 (MQ=255)

                                                                                                     accTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGAc                                                          <  2:212494/81‑1 (MQ=255)

                                                                                                     accTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGAc                                                          >  1:212494/1‑81 (MQ=255)

                                                                                                     accTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACt       >  1:933493/1‑132 (MQ=255)

                                                                                                     accTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACt       <  2:933493/132‑1 (MQ=255)

||

CTGCGGTAATGGCTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACCTGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGAT  >  NC_000913/2416632‑2416869

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A