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 F28 I1 R1	139	58.0	1973578	98.9%	1951868	138.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,419,006	T→C	intergenic (+395/‑36)	yhdV → / → yhdW	lipoprotein YhdV/putative ABC transporter periplasmic binding protein YhdW

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,419,006	0	T	C	100.0%	142.3 / NA	40	intergenic (+395/‑36)	yhdV/yhdW	lipoprotein YhdV/putative ABC transporter periplasmic binding protein YhdW
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (18/22); total (18/22)

CGCTGTTTTTATTATTTCCTGTCTACACTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGTCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAA  >  NC_000913/3418883‑3419141

cgcTGTTTTTATTATTTCCTGTCTACACTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAAttt                                                                                                                         >  1:216280/1‑140 (MQ=255)

   tGTTTTTATTATTTCCTGTCTACACTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCg                                                                                                                      <  1:308442/140‑1 (MQ=255)

   tGTTTTTATTATTTCCTGTCTACACTCAGCTTATTGCGACGCGAAATCGGGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCg                                                                                                                      >  2:106858/1‑140 (MQ=255)

     tttttATTATTTCCTGTCTACACTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGcc                                                                                                                    <  2:543750/140‑1 (MQ=255)

      ttttATTATTTCCTGTCTACACTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCt                                                                                                                   <  1:733318/140‑1 (MQ=255)

                 ccTGTCTACACTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCa                                                                                                        <  1:486784/140‑1 (MQ=255)

                   tGTCTACACTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCAtt                                                                                                      <  1:106858/140‑1 (MQ=255)

                        acacTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGaa                                                                                                 <  2:456574/140‑1 (MQ=255)

                             cAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAga                                                                                            <  2:418124/140‑1 (MQ=255)

                               gCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCa                                                                                                        >  2:825881/1‑126 (MQ=255)

                               gCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCa                                                                                                        <  1:825881/126‑1 (MQ=255)

                               gCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAgatg                                                                                          >  1:294196/1‑140 (MQ=255)

                               gCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAgatg                                                                                          >  2:480463/1‑140 (MQ=255)

                               gCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAgatg                                                                                          >  1:747775/1‑140 (MQ=255)

                               gCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAgatg                                                                                          >  1:801296/1‑140 (MQ=255)

                                 ttATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAgatgat                                                                                        <  1:873103/140‑1 (MQ=255)

                                   aTTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAgatgatga                                                                                      >  2:605299/1‑140 (MQ=255)

                                   aTTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAgatgatga                                                                                      <  2:153218/140‑1 (MQ=255)

                                     tGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATa                                                                                    >  1:593092/1‑140 (MQ=255)

                                          cgcgAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCcac                                                                               >  1:879923/1‑140 (MQ=255)

                                            cgAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCacac                                                                             <  2:563272/140‑1 (MQ=255)

                                            cgAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCacac                                                                             <  1:480463/140‑1 (MQ=255)

                                            cgAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCacac                                                                             <  1:101656/140‑1 (MQ=255)

                                            cgAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCacac                                                                             <  1:551602/140‑1 (MQ=255)

                                                                     tactTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACGGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGc                                                    <  2:388843/140‑1 (MQ=255)

                                                                        ttttGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGt                                                 <  2:813256/140‑1 (MQ=255)

                                                                           tGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTgctgct                                                       >  2:352290/1‑131 (MQ=255)

                                                                           tGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTgctgct                                                       <  1:352290/131‑1 (MQ=255)

                                                                           tGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGc                                              >  2:293630/1‑140 (MQ=255)

                                                                           tGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGc                                              >  1:822178/1‑140 (MQ=255)

                                                                               tataAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCAGCCAGCGTGCTGCTTGCCGTTGCAAAt                                          <  2:747775/140‑1 (MQ=255)

                                                                                          ggCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAgg                                      >  1:751928/1‑133 (MQ=255)

                                                                                          ggCCACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAgg                                      <  2:751928/133‑1 (MQ=255)

                                                                                            ccACAGACAGGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTgg                             >  1:765299/1‑140 (MQ=255)

                                                                                                agacagGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGcgcg                         <  1:195928/140‑1 (MQ=255)

                                                                                                  acagGTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGAc                       >  1:4247/1‑140 (MQ=255)

                                                                                                      gTAAAAGACGTTTCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCtt                   >  1:633564/1‑140 (MQ=255)

                                                                                                                tttCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTc         >  2:980292/1‑140 (MQ=255)

                                                                                                                tttCCCAAACGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTc         <  2:392094/140‑1 (MQ=255)

                                                                                                                       aaCGCCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGaaaaa  <  2:241612/140‑1 (MQ=255)

CGCTGTTTTTATTATTTCCTGTCTACACTCAGCTTATTGCGACGCGAAATCGTGCGCAAAAGCTGGCACTACTTTTGCTTATAAGAGGATGGCCACAGACAGGTAAAAGACGTTTCCCAAACGTCCTATAACGATAATTTTCGCCTCACAGGAAGCATTATGAAAAAGATGATGATAGCCACACTGGCTGCCGCCAGCGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAAA  >  NC_000913/3418883‑3419141

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