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
A4 F28 I1 R1	159	82.1	2830106	99.3%	2810295	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,227,340	(C)_6→7	pseudogene (1419/1436 nt)	mdtQ ←	putative multidrug resistance outer membrane protein MdtQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,227,334	1	.	C	100.0%	171.6 / NA	47	pseudogene (1425/1436 nt)	mdtQ	putative multidrug resistance outer membrane protein MdtQ
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (22/25); total (22/25)

CCTGCTGCGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAGCAATGATGCCCGCG  >  NC_000913/2227195‑2227467

ccTGCTGCGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTa                                                                                                                                        <  1:1036786/140‑1 (MQ=255)

ccTGCTGCGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTa                                                                                                                                        <  2:1397105/140‑1 (MQ=255)

  tgctgcGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑cc                                                                                                                                     >  2:367509/1‑140 (MQ=255)

        gcCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑cccccccg                                                                                                                               <  1:786424/140‑3 (MQ=255)

          cAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑cccccccgcc                                                                                                                             <  2:690596/140‑5 (MQ=255)

            gTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCa                                                                                                                            >  1:806308/1‑140 (MQ=255)

            gTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCa                                                                                                                            <  1:509132/140‑1 (MQ=255)

            gTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCa                                                                                                                            <  1:260546/140‑1 (MQ=255)

               ataaCGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACg                                                                                                                         <  2:378350/140‑1 (MQ=255)

                 aaCGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGGTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCa                                                                                                                       <  2:45374/140‑1 (MQ=255)

                 aaCGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCa                                                                                                                       <  1:367509/140‑1 (MQ=255)

                   cgcgCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCAcc                                                                                                                     >  2:1055391/1‑140 (MQ=255)

                    gcgcACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCa                                                                                                                    <  1:1384101/140‑1 (MQ=255)

                     cgcACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAg                                                                                                                   >  1:442524/1‑140 (MQ=255)

                      gcACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCCACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGCATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGt                                                                                                                  >  2:1219994/1‑140 (MQ=255)

                       cACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCa                                                                                                                    >  2:655720/1‑137 (MQ=255)

                       cACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCa                                                                                                                    <  1:655720/137‑1 (MQ=255)

                       cACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTg                                                                                                                 >  1:845786/1‑140 (MQ=255)

                         ctctTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAg                                                                                                               <  2:717285/140‑1 (MQ=255)

                                      cccGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCa                                                                                                  >  2:1024621/1‑140 (MQ=255)

                                             cGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGcc                                                                                           <  2:845786/140‑1 (MQ=255)

                                               gAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCAc                                                                                         >  2:581951/1‑140 (MQ=255)

                                                   cGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc                                                                                     <  1:857638/140‑1 (MQ=255)

                                                   cGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc                                                                                     <  1:1142711/140‑1 (MQ=255)

                                                   cGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc                                                                                     <  2:301713/140‑1 (MQ=255)

                                                     gTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCt                                                                                   <  1:166935/140‑1 (MQ=255)

                                                        ataatCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGc                                                                                <  2:597866/140‑1 (MQ=255)

                                                                aaCCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGTATGGAGGCATCCAGCCACTGCCCTTGCAATAACAg                                                                        >  1:963201/1‑140 (MQ=255)

                                                                        ccATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTgg                                                                <  1:642938/140‑1 (MQ=255)

                                                                        ccATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTgg                                                                <  2:66954/140‑1 (MQ=255)

                                                                                  ctcCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACg                                                      <  1:1024621/140‑1 (MQ=255)

                                                                                  ctcCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACg                                                      <  2:442524/140‑1 (MQ=255)

                                                                                         tAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGTATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGcgcg                                               <  2:963201/140‑1 (MQ=255)

                                                                                                                 aGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCgg                       >  2:1237849/1‑140 (MQ=255)

                                                                                                                  gAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCggg                      <  1:511956/140‑1 (MQ=255)

                                                                                                                   aaGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGa                     <  1:48692/140‑1 (MQ=255)

                                                                                                                   aaGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGa                     <  1:581951/140‑1 (MQ=255)

                                                                                                                       cgcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGAcgcg                        >  1:805729/1‑133 (MQ=255)

                                                                                                                       cgcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGAcgcg                        <  2:805729/133‑1 (MQ=255)

                                                                                                                       cgcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCa                 >  2:783171/1‑140 (MQ=255)

                                                                                                                        gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAAc                   >  2:870711/1‑137 (MQ=255)

                                                                                                                        gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAAc                   <  1:870711/137‑1 (MQ=255)

                                                                                                                        gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAg                >  2:1398489/1‑140 (MQ=255)

                                                                                                                        gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAg                >  1:1140353/1‑140 (MQ=255)

                                                                                                                        gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAg                >  2:1382495/1‑140 (MQ=255)

                                                                                                                        gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAg                >  2:192631/1‑140 (MQ=255)

                                                                                                                                 caGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAGCAATGATGc       >  1:938008/1‑140 (MQ=255)

                                                                                                                                    cGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGa                     >  1:633269/1‑123 (MQ=255)

                                                                                                                                    cGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGa                     <  2:633269/123‑1 (MQ=255)

                                                                                                                                    cGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCACGGGGATTCTGTCTTCGATGACGCGGCCACCAGCAATGATGcccc    >  2:877041/1‑139 (MQ=255)

                                                                                                                                      tttGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAGCAATGATGCCcgcg  >  1:1287568/1‑140 (MQ=255)

                                                                                                                                      tttGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAGCAATGATGCCcgcg  >  1:172946/1‑140 (MQ=255)

CCTGCTGCGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAGCAATGATGCCCGCG  >  NC_000913/2227195‑2227467

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A