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
A10 F1 I1 R1	759	65.2	3386260	90.7%	3071337	101.6

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%	127.4 / NA	40	L673S (CTG→TCG)	pta	phosphate acetyltransferase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (23/17); total (23/17)
*	NC_000913	2,416,764	0	T	C	100.0%	143.1 / NA	40	L673S (CTG→TCG)	pta	phosphate acetyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (23/17); total (23/17)

GCTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACCTGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCAGTCTGCACAGC  >  NC_000913/2416643‑2416883

||

gCTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGa                                                                                                        <  2:1268961/139‑1 (MQ=255)

 cTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGAt                                                                                                       <  2:349937/139‑1 (MQ=255)

          cGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAggg                                                                                              >  1:687889/1‑139 (MQ=255)

                                tcCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCg                                                                                                         >  2:1158037/1‑106 (MQ=255)

                                tcCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCg                                                                                                         <  1:1158037/106‑1 (MQ=255)

                                                       tgtTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGa                                                 >  2:94144/1‑139 (MQ=255)

                                                            aTCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGata                                            <  2:687889/139‑1 (MQ=255)

                                                              cTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATc                                          >  2:937368/1‑139 (MQ=255)

                                                              cTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATc                                          <  1:94144/139‑1 (MQ=255)

                                                                   cGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTa                                     >  1:935903/1‑139 (MQ=255)

                                                                          gAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATc                              >  2:1509753/1‑139 (MQ=255)

                                                                           aaCACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCAc                                                        <  2:886898/112‑1 (MQ=255)

                                                                           aaCACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCAc                                                        >  1:886898/1‑112 (MQ=255)

                                                                           aaCACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATcg                             >  2:1227589/1‑139 (MQ=255)

                                                                                cGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGa                                                                                                        <  2:162302/59‑1 (MQ=255)

                                                                                cGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGa                                                                                                        >  1:162302/1‑59 (MQ=255)

                                                                                cGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGAGGATATCGTCTACACCATCGCGCTg                        >  1:945495/1‑139 (MQ=255)

                                                                                cGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGata                                            >  2:524562/1‑119 (MQ=255)

                                                                                cGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGata                                            <  1:524562/119‑1 (MQ=255)

                                                                                cGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGC‑GGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGa                       >  1:328947/1‑139 (MQ=255)

                                                                                  gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGc                                                                                                           >  2:1137939/1‑54 (MQ=255)

                                                                                  gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGc                                                                                                           <  1:1137939/54‑1 (MQ=255)

                                                                                  gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCg                                                                                                         >  1:1176302/1‑56 (MQ=255)

                                                                                  gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCg                                                                                                         <  2:1176302/56‑1 (MQ=255)

                                                                                  gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATc                                          <  2:996282/119‑1 (MQ=255)

                                                                                  gTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATc                                          >  1:996282/1‑119 (MQ=255)

                                                                                   tAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACt                     <  1:1227589/139‑1 (MQ=255)

                                                                                     acacCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGc                                                                                                           <  2:1484303/51‑1 (MQ=255)

                                                                                     acacCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGc                                                                                                           >  1:1484303/1‑51 (MQ=255)

                                                                                     acacCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCg                                                                                                         <  2:1665249/53‑1 (MQ=255)

                                                                                     acacCACCTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCg                                                                                                         >  1:1665249/1‑53 (MQ=255)

                                                                                           ccTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCa             >  2:402665/1‑139 (MQ=255)

                                                                                            cTACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCAg            >  1:346796/1‑139 (MQ=255)

                                                                                             tACAAAGCGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCAGt           >  1:621418/1‑139 (MQ=255)

                                                                                                    cGGTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTCGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCAGTCTGcaca    >  2:86877/1‑139 (MQ=255)

                                                                                                     ggTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCAGTCTGCAcag   <  1:86877/139‑1 (MQ=255)

                                                                                                     ggTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCAGTCTGCAcag   <  1:1078751/139‑1 (MQ=255)

                                                                                                      gTACAGCGTTCTGCCGACTCGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCAGTCTGCAcagc  >  2:1029499/1‑139 (MQ=255)

                                                                                                            cGTTCTGCCGACTCGATCTCCATCGGGCCGAtgctg                                                                                                   >  1:722242/1‑36 (MQ=255)

                                                                                                            cGTTCTGCCGACTCGATCTCCATCGGGCCGAtgctg                                                                                                   <  2:722242/36‑1 (MQ=255)

||

GCTGACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGTACAGCGTTCTGCCGACCTGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTCTACACCATCGCGCTGACTGCGATTCAGTCTGCACAGC  >  NC_000913/2416643‑2416883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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