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 F1 I1 R1	83	73.5	3575638	92.3%	3300313	107.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,142,011	C→T	A71T (GCC→ACC)	frwA ←	putative PTS enzyme: Hpr, enzyme I and II components

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,142,011	0	C	T	100.0%	186.1 / NA	54	A71T (GCC→ACC)	frwA	putative PTS enzyme: Hpr, enzyme I and II components
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (23/31); total (23/31)

CGGATTCAGATTGGTCAGTGAAACCGGCAGTGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGCCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTGCGCAGGTTATGCCACTCAATTTGTGATGAAAAAGTATTACA  >  NC_000913/4141877‑4142143

cGGATTCAGATTGGTCAGTGAAACCGGCAGTGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCg                                                                                                                                  <  1:638170/139‑1 (MQ=255)

         aTTGGTCAGTGAAACCGGCAGTGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGt                                                                                                                         <  2:1773592/139‑1 (MQ=255)

                   gAAACCGGCAGTGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGt                                                                                                               <  2:1235181/139‑1 (MQ=255)

                       ccGGCAGTGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAACCGCTGGGGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATc                                                                                                           <  1:389710/139‑1 (MQ=255)

                        cGGCAGTGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATcg                                                                                                          >  1:1150516/1‑139 (MQ=255)

                            aGTGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATcgcccg                                                                                                      <  2:933901/139‑1 (MQ=255)

                              tGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATcgcccgcc                                                                                                    >  1:445271/1‑139 (MQ=255)

                                     aGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTAt                                                                                             <  1:1318967/139‑1 (MQ=255)

                                        tCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTa                                                                                                                        <  2:1094020/109‑1 (MQ=255)

                                        tCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTa                                                                                                                        >  1:1094020/1‑109 (MQ=255)

                                           tCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATcgcc                                                                                                        >  2:1688106/1‑122 (MQ=255)

                                           tCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATcgcc                                                                                                        <  1:1688106/122‑1 (MQ=255)

                                               aTTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGt                                                                                                               >  1:1315755/1‑111 (MQ=255)

                                               aTTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGt                                                                                                               <  2:1315755/111‑1 (MQ=255)

                                                   aaCTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCgg                                                                                                                                 <  2:817853/89‑1 (MQ=255)

                                                   aaCTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCgg                                                                                                                                 >  1:817853/1‑89 (MQ=255)

                                                         cGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCa                                                                                                   >  1:885403/1‑113 (MQ=255)

                                                         cGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCa                                                                                                   <  2:885403/113‑1 (MQ=255)

                                                         cGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAgg                                                                         >  2:1686417/1‑139 (MQ=255)

                                                               cggcgCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCtt                                                                   >  2:1082906/1‑139 (MQ=255)

                                                               cggcgCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCtt                                                                   <  1:256803/139‑1 (MQ=255)

                                                                    cATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGc                                                              >  2:1233148/1‑139 (MQ=255)

                                                                                  aaTTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGt                                                <  2:1619799/139‑1 (MQ=255)

                                                                                  aaTTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGt                                                <  1:1233148/139‑1 (MQ=255)

                                                                                   aTTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGt                                                            >  1:555328/1‑126 (MQ=255)

                                                                                   aTTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGt                                                            <  2:555328/126‑1 (MQ=255)

                                                                                    ttCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCa                                              >  1:1099685/1‑139 (MQ=255)

                                                                                    ttCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCa                                              >  1:39073/1‑139 (MQ=255)

                                                                                    ttCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCa                                              <  1:1686417/139‑1 (MQ=255)

                                                                                         cgcgCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         >  1:1423073/1‑139 (MQ=255)

                                                                                         cgcgCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         <  2:1613879/139‑1 (MQ=255)

                                                                                         cgcgCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         <  2:1763220/139‑1 (MQ=255)

                                                                                         cgcgCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         <  2:1423073/139‑1 (MQ=255)

                                                                                         cgcgCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         <  2:1099685/139‑1 (MQ=255)

                                                                                                       cTTAAACGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGTGGTCAGTGCGCAGGTTATGCCACt                           <  2:1150516/139‑1 (MQ=255)

                                                                                                          aaaCGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATc                                                                                                           <  1:1007994/56‑1 (MQ=255)

                                                                                                          aaaCGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATc                                                                                                           >  2:1007994/1‑56 (MQ=255)

                                                                                                          aaaCGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCACCCGCCAGCGTATCGGTg                                                                                        >  1:1758830/1‑75 (MQ=255)

                                                                                                          aaaCGCTGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCACCCGCCAGCGTATCGGTg                                                                                        <  2:1758830/75‑1 (MQ=255)

                                                                                                                tGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         >  2:520459/1‑116 (MQ=255)

                                                                                                                tGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         <  2:1486349/116‑1 (MQ=255)

                                                                                                                tGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         >  1:1486349/1‑116 (MQ=255)

                                                                                                                tGGTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTGCGCAGGTTATGCCACTCAATTtgtg                  >  1:1672751/1‑139 (MQ=255)

                                                                                                                tGGTGCGCTGCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         <  1:520459/116‑1 (MQ=255)

                                                                                                                  gTGCGCTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTGCGCAGGTTATGCCACTCAATTTGtgat                >  2:764091/1‑139 (MQ=255)

                                                                                                                     cgcTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTgg                                                                                                                   >  2:568573/1‑37 (MQ=255)

                                                                                                                     cgcTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTgg                                                                                                                   <  1:568573/37‑1 (MQ=38)

                                                                                                                       cTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCTAATCAgcgc                                                                             >  1:1161722/1‑73 (MQ=255)

                                                                                                                       cTTCCTGTTCGTCGGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCTATCAgcgc                                                                             <  2:1161722/73‑1 (MQ=255)

                                                                                                                               tcgtcgGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATGAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTGCGCAGGTTATGCCACTCAATTTGTGATGAAAAAGTATTac   <  1:1082906/139‑1 (MQ=255)

                                                                                                                                cgtcgGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTGCGCAGGTTATGCCACTCAATTTGTGATGAAAAAGTATTaca  <  2:1485303/139‑1 (MQ=255)

                                                                                                                                cgtcgGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTGCGCAGGTTATGCCACTCAATTTGTGATGAAAAAGTATTaca  <  2:39073/139‑1 (MQ=255)

                                                                                                                                  tcgGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         <  2:231420/98‑1 (MQ=255)

                                                                                                                                  tcgGTCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTgcg                                         >  1:231420/1‑98 (MQ=255)

CGGATTCAGATTGGTCAGTGAAACCGGCAGTGGTTCCAGTTCGTCAGATTTAACTTCCGCCAGCGGCGCATCGCAGTGGGGGAATTCATCGCGCAGCCATTGGCTTAAACGCTGGTGCGCTTCCTGTTCGTCGGCCCCGGAAATCAGTAACTGGCAGTTATCGCCCGCCAGCGTATCGGTGCCAATCAGCGCAAGGGCGCTTTTGGCGTTGCCCTTGCGGTCAGTGCGCAGGTTATGCCACTCAATTTGTGATGAAAAAGTATTACA  >  NC_000913/4141877‑4142143

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 28 ≤` `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