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
A2 F1 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,344,045	G→A	L34L (CTG→CTA)	lptB →	lipopolysaccharide export ABC transporter ATPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,344,045	0	G	A	100.0%	123.3 / NA	36	L34L (CTG→CTA)	lptB	lipopolysaccharide export ABC transporter ATPase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (19/17); total (19/17)

GGCACAGAAGAAGGGTAATTAATTCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTGCTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCTGCTGCCTCTGCATGCACGCGCGCGCCGCGG  >  NC_000913/3343916‑3344179

ggCACAGAAGAAGGGTAATTAATTCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCa                                                                                                                               >  2:585418/1‑139 (MQ=255)

ggCACAGAAGAAGGGTAATTAATTCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCa                                                                                                                               >  1:86027/1‑139 (MQ=255)

                 attaattCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGac                                                                                                              >  2:503177/1‑139 (MQ=255)

                 attaattCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGac                                                                                                              >  2:38201/1‑139 (MQ=255)

                   taattCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTg                                                                                                                        >  2:564808/1‑127 (MQ=255)

                   taattCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTg                                                                                                                        <  1:564808/127‑1 (MQ=255)

                    aattCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGaccac                                                                                                           >  1:644783/1‑139 (MQ=255)

                               gCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACa                                                                                                <  2:86027/139‑1 (MQ=255)

                               gCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACa                                                                                                <  1:503177/139‑1 (MQ=255)

                                      tAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGt                                                                                         <  2:533727/139‑1 (MQ=255)

                                           gCAAAGAACCTTGCAAAAGCATATGAGGGCCGTGGGGTGGTAGAAGGCGTCAGCCTGGCCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCGAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCa                                                                                    <  1:223112/139‑1 (MQ=255)

                                                    cTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCcgc                                                                           >  2:428953/1‑139 (MQ=255)

                                                      tGCAAAAGCCTATAAAGGCCGTCGTGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGt                                                                                                                   >  2:39555/1‑97 (MQ=255)

                                                      tGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGt                                                                                                                   <  1:39555/97‑1 (MQ=255)

                                                      tGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCcgcgc                                                                         >  1:574701/1‑139 (MQ=255)

                                                          aaaGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATg                                                                     <  1:38201/139‑1 (MQ=255)

                                                                  taAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAAc                                                             <  2:644783/139‑1 (MQ=255)

                                                                       gCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGacca                                                                                                            >  1:530901/1‑87 (MQ=255)

                                                                       gCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGacca                                                                                                            <  2:530901/87‑1 (MQ=255)

                                                                        ccGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCatt                                                       >  2:534031/1‑139 (MQ=255)

                                                                          gTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCattat                                                     >  1:314967/1‑139 (MQ=255)

                                                                          gTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCattat                                                     >  2:220003/1‑139 (MQ=255)

                                                                                         aCGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGatat                                      <  1:428953/139‑1 (MQ=255)

                                                                                             cAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATc                                     >  2:344561/1‑136 (MQ=255)

                                                                                             cAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATc                                     <  1:344561/136‑1 (MQ=255)

                                                                                             cAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGt                                  >  2:648089/1‑139 (MQ=255)

                                                                                                ccTGACCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTctg                               >  2:107387/1‑139 (MQ=255)

                                                                                                    aCCGTCAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCtgctgc                           <  2:314967/139‑1 (MQ=255)

                                                                                                         cAACTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCTGCTGCCTCtg                      >  1:13431/1‑139 (MQ=255)

                                                                                                           aCTCCGGGGAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCTGCTGCCTCtgca                    >  2:572555/1‑139 (MQ=255)

                                                                                                                ggggAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCaa                                                              <  2:371462/92‑1 (MQ=255)

                                                                                                                ggggAAATTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCaa                                                              >  1:371462/1‑92 (MQ=255)

                                                                                                                      aTTGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCTGCTGCCTCTGCATGCAcgcgcgc         <  2:362313/139‑1 (MQ=255)

                                                                                                                       ttGTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCTGCTGCCTCTGCATGCAcgcgcgcg        <  1:107387/139‑1 (MQ=255)

                                                                                                                         gTCGGTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCTGCTGCCTCTGCATGCACGCGCGcgcc      <  1:585418/139‑1 (MQ=255)

                                                                                                                             gTCTACTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCTGCTGCCTCTGCATGCACGCGCGCGCCACgg  <  2:574701/139‑1 (MQ=255)

GGCACAGAAGAAGGGTAATTAATTCGTTATGGCAACATTAACTGCAAAGAACCTTGCAAAAGCCTATAAAGGCCGTCGCGTGGTAGAAGACGTCAGCCTGACCGTCAACTCCGGGGAAATTGTCGGTCTGCTGGGGCCAAACGGTGCCGGTAAGACCACCACTTTCTACATGGTTGTAGGCATTGTGCCGCGCGATGCGGGCAACATCATTATTGATGATGACGATATCAGTCTGCTGCCTCTGCATGCACGCGCGCGCCGCGG  >  NC_000913/3343916‑3344179

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