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	776	60.0	3074904	90.1%	2770488	104.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,316,789	C→T	R145H (CGT→CAT)	trpA ←	tryptophan synthase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,316,789	0	C	T	100.0%	139.4 / NA	45	R145H (CGT→CAT)	trpA	tryptophan synthase, alpha subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (19/26); total (19/26)

CGGCGCGGTTTTCTGCGCCGGTCACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGACGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAACACCAGATTGGCA  >  NC_000913/1316655‑1316917

cggcgcggTTTTCTGCGCCGGTCACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCaa                                                                                                                              >  1:227367/1‑139 (MQ=255)

 ggcgcggTTTTCTGCGCCGGTCACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAAc                                                                                                                             >  1:1139392/1‑139 (MQ=255)

       gTTTTCTGCGCCGGTCACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGcc                                                                                                                       <  2:833015/139‑1 (MQ=255)

              gcgcCGGTCACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGa                                                                                                                <  2:319489/139‑1 (MQ=255)

                  cGGTCACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAggg                                                                                                            <  1:1525971/139‑1 (MQ=255)

                   ggTCACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGgc                                                                                                           <  2:1486324/139‑1 (MQ=255)

                      cACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGcgcg                                                                                                        <  2:1259684/139‑1 (MQ=255)

                              cTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTc                                                                                                >  1:1239664/1‑139 (MQ=255)

                                      aGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGca                                                                                        <  2:268151/139‑1 (MQ=255)

                                                          aCCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGActc                                                                                                   >  2:959819/1‑108 (MQ=255)

                                                          aCCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGActc                                                                                                   <  1:959819/108‑1 (MQ=255)

                                                            cGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGaa                                                                                                               <  1:439763/94‑1 (MQ=255)

                                                            cGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGaa                                                                                                               >  2:439763/1‑94 (MQ=255)

                                                              tAAGAGGCTATCTGGCGGAGCAGGTCGTCATCGGCCTTTGGCGGGCTGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCACCTGGCACATCGGCAACCAGCACCGAATcca                                                                >  1:909767/1‑137 (MQ=255)

                                                              tAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGa                                                                >  1:110962/1‑139 (MQ=255)

                                                              tAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGa                                                                >  1:770922/1‑139 (MQ=255)

                                                                        tCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACttt                                                      >  1:589867/1‑139 (MQ=255)

                                                                         cTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACtttt                                                     <  1:532954/139‑1 (MQ=255)

                                                                              gcagcaGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCa                                                <  1:74683/139‑1 (MQ=255)

                                                                                  cagGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTgg                                            >  2:1347231/1‑139 (MQ=255)

                                                                                     gtcgtcATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCa                                         <  1:184671/139‑1 (MQ=255)

                                                                                     gtcgtcATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCa                                         <  1:1252826/139‑1 (MQ=255)

                                                                                              ggCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGcgcg                                                                                                        <  2:1346183/67‑1 (MQ=255)

                                                                                              ggCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGcgcg                                                                                                        >  1:1346183/1‑67 (MQ=255)

                                                                                                cATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACtcatc                              <  2:324905/139‑1 (MQ=255)

                                                                                                   ttGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAAt                           >  2:867993/1‑139 (MQ=255)

                                                                                                    tGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCaa                            <  1:565892/137‑1 (MQ=255)

                                                                                                    tGGCGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCaa                            >  2:565892/1‑137 (MQ=255)

                                                                                                       cGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATaaaa                                    <  2:1245393/126‑1 (MQ=255)

                                                                                                       cGGGCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATaaaa                                    >  1:1245393/1‑126 (MQ=255)

                                                                                                        gggCAGATGAAGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCtt                      <  2:589867/139‑1 (MQ=255)

                                                                                                                  aGATAGGTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAacac            <  2:227367/139‑1 (MQ=255)

                                                                                                                        gTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGcgcg                                                                                                        >  2:872158/1‑41 (MQ=255)

                                                                                                                        gTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGcgcg                                                                                                        <  1:872158/41‑1 (MQ=255)

                                                                                                                        gTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAACACCAGa        >  1:157254/1‑137 (MQ=255)

                                                                                                                        gTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAACACCAGa        <  2:157254/137‑1 (MQ=255)

                                                                                                                        gTGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAACACCAGAtt      >  1:767533/1‑139 (MQ=255)

                                                                                                                         tGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACg                                                              >  1:707240/1‑82 (MQ=255)

                                                                                                                         tGCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACg                                                              <  2:707240/82‑1 (MQ=255)

                                                                                                                          gCGACATTATGATGCAACGCGGCCTTGGGGAAGGGCGCGGACTCTTCAACGGGCACATCTGCAACCAGCAGCGAATCGACGCCGACTTTTTAGCACTGAGCATAAAACTCATCAATGCCTTTGTTAAACACCAGATTgg    <  2:909767/139‑1 (MQ=255)

                                                                                                                          gCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAACACCAGATTgg    <  2:110962/139‑1 (MQ=255)

                                                                                                                          gCGACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAACACCAGATTgg    <  1:655703/139‑1 (MQ=255)

                                                                                                                            gACATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAACACCAGATTGGCa  <  1:1347231/139‑1 (MQ=255)

                                                                                                                              cATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAAc                                                                              <  2:1370175/61‑1 (MQ=255)

                                                                                                                              cATTATGATGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAAc                                                                              >  1:1370175/1‑61 (MQ=255)

CGGCGCGGTTTTCTGCGCCGGTCACGCCTGCTCGTGACAGCAAATAGGTGTAACCACGACCGTAAGAGGCTATCTGGCGCAGCAGGTCGTCATCGGCATTTGGCGGGCAGATGAAGATAGGTGCGACATTATGACGCAACGCGGCCTGGCGGAAGGGCGCGGACTCTTCAACTGGCACATCGGCAACCAGCACCGAATCGACGCCGACTTTTTCGCACTGGGCATAAAACTCATCAATGCCTTTGTTAAACACCAGATTGGCA  >  NC_000913/1316655‑1316917

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A