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
A5 F1 I2 R1	772	77.0	3769570	91.6%	3452926	105.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,062,401	T→C	Q308R (CAG→CGG)	ldtA ←	L,D‑transpeptidase linking Lpp to murein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,062,401	0	T	C	100.0%	188.5 / NA	53	Q308R (CAG→CGG)	ldtA	L,D‑transpeptidase linking Lpp to murein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (25/28); total (25/28)

TGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCTGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCAAAGATGGGGTTACCGGC  >  NC_000913/2062265‑2062520

tGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGt                                                                                                                       >  1:1067370/1‑139 (MQ=255)

  tAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCt                                                                                                                     >  2:900376/1‑139 (MQ=255)

            ggTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGaa                                                                                                           <  1:247778/139‑1 (MQ=255)

                   cggcggACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAAttt                                                                                                    >  1:834427/1‑139 (MQ=255)

                    ggcggACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAAt                                                                                                      <  2:212618/136‑1 (MQ=255)

                    ggcggACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAAt                                                                                                      >  1:212618/1‑136 (MQ=255)

                      cggACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGca                                                                                                 <  2:589714/139‑1 (MQ=255)

                      cggACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGca                                                                                                 >  1:238080/1‑139 (MQ=255)

                       ggACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGcac                                                                                                <  2:834427/139‑1 (MQ=255)

                        gACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGcaca                                                                                               >  1:1304447/1‑139 (MQ=255)

                                    gTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGAt                                                                                   <  1:1872987/139‑1 (MQ=255)

                                            cTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTg                                                                           >  2:1210018/1‑139 (MQ=255)

                                            cTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTg                                                                           >  1:1118219/1‑139 (MQ=255)

                                                           tCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTgc                                                            <  1:900376/139‑1 (MQ=255)

                                                            cAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTgcg                                                           <  2:583827/139‑1 (MQ=255)

                                                               aggagCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGa                                                        >  1:1011093/1‑139 (MQ=255)

                                                                 gagCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGAtt                                                      <  2:1609451/139‑1 (MQ=255)

                                                                  agCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGAttt                                                     <  2:97140/139‑1 (MQ=255)

                                                                         ttCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCaa                                              >  2:239798/1‑139 (MQ=255)

                                                                                 aGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGc                                      <  1:1397078/139‑1 (MQ=255)

                                                                                      gCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGtt                                 >  2:1037810/1‑139 (MQ=255)

                                                                                            tAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATaaa                           <  1:1037810/139‑1 (MQ=255)

                                                                                               cAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGc                        <  2:238080/139‑1 (MQ=255)

                                                                                                 ggCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCAt                                                                                          <  2:1827896/71‑1 (MQ=255)

                                                                                                 ggCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCAt                                                                                          >  1:1716159/1‑71 (MQ=255)

                                                                                                 ggCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCAt                                                                                          <  2:1716159/71‑1 (MQ=255)

                                                                                                 ggCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCAt                                                                                          >  1:1827896/1‑71 (MQ=255)

                                                                                                 ggCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGa                                                        <  2:1062469/105‑1 (MQ=255)

                                                                                                 ggCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGa                                                        >  1:1062469/1‑105 (MQ=255)

                                                                                                 ggCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGccc                      <  2:1304447/139‑1 (MQ=255)

                                                                                                            ttCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATaaa                           >  2:1376994/1‑123 (MQ=255)

                                                                                                            ttCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATaaa                           <  1:1376994/123‑1 (MQ=255)

                                                                                                            ttCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATaaa                           <  1:374501/123‑1 (MQ=255)

                                                                                                            ttCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATaaa                           >  2:374501/1‑123 (MQ=255)

                                                                                                             tCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTgcg                                                           <  2:461815/90‑1 (MQ=255)

                                                                                                             tCTAATTACCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTgcg                                                           >  1:461815/1‑90 (MQ=255)

                                                                                                                    aCCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGAt                                                                                   >  1:369733/1‑59 (MQ=255)

                                                                                                                    aCCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGAt                                                                                   <  2:369733/59‑1 (MQ=255)

                                                                                                                    aCCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGAttt                                                     <  2:313090/89‑1 (MQ=255)

                                                                                                                    aCCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGAttt                                                     >  1:313090/1‑89 (MQ=255)

                                                                                                                    aCCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCAAAGATgggg          <  2:333647/132‑1 (MQ=255)

                                                                                                                    aCCAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCAAAGATgggg          >  1:333647/1‑132 (MQ=255)

                                                                                                                     ccAACGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCAAAGATGGGGTTACCGGc  <  1:239798/139‑1 (MQ=255)

                                                                                                                         cGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGc                                                                                                  <  1:619643/39‑1 (MQ=255)

                                                                                                                         cGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGc                                                                                                  >  2:619643/1‑39 (MQ=255)

                                                                                                                         cGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATc                                                >  1:67392/1‑89 (MQ=255)

                                                                                                                         cGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATc                                                <  2:67392/89‑1 (MQ=255)

                                                                                                                         cGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATaaa                           >  2:285867/1‑110 (MQ=255)

                                                                                                                         cGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATaaa                           <  1:285867/110‑1 (MQ=255)

                                                                                                                         cGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCa                   >  1:1798425/1‑118 (MQ=255)

                                                                                                                         cGCTCTTAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCa                   <  2:1798425/118‑1 (MQ=255)

                                                                                                                              ttAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCAAAGATg             >  2:397282/1‑119 (MQ=255)

                                                                                                                              ttAAAACATCCGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCAAAGATg             <  1:397282/119‑1 (MQ=255)

TGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTCAAAAAAGCCTGCTTTCTAGCAGGCTTTTTGCTTTCTAATTACCAACGCTCTTAAAACATCTGTCTTGAACCAGAACTAATTTGCACAGGCATTCCCGATCGACGTTGCAACGCAGCATTTGCGCGATTTACATCAACTTCTTGCCCGTTGATAAACGCCCGCAAAGATGGGGTTACCGGC  >  NC_000913/2062265‑2062520

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A