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
A14 F68 I0 R1	683	78.3	2772122	98.0%	2716679	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,171,814	A→G	8.0%	intergenic (‑87/+19)	gatR ← / ← gatD	pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted/galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,171,814	0	A	G	8.0%	153.7 / 4.1	50	intergenic (‑87/+19)	gatR/gatD	pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted/galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding
Reads supporting (aligned to +/- strand): ref base A (26/20); new base G (2/2); total (28/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.56e-01

AGCACGGTTCCCTGTTCATTCACTAATTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACTTACGTTCTGTCAGCA  >  NC_000913/2171666‑2171960

aGCACGGTTCCCTGTTCATTCACTAATTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCa                                                                                                                                                    <  4:647839/149‑1 (MQ=255)

aGCACGGTCCCCTGTTCATTCACTAATTGGATGATTTTATTCCTTCGCTCGAATGACTTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACACTTGGTGCATGATCTGTTTTGCACAATACCGGGCCAGCa                                                                                                                                                    >  2:687964/1‑149 (MQ=255)

           cTGTTCATTCACTAATTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGcc                                                                                                                                         <  2:60764/149‑1 (MQ=255)

           cTGTTCATTCACTAATTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGcc                                                                                                                                         >  1:65407/1‑149 (MQ=255)

            tGTTCATTCACTAATTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGccc                                                                                                                                        >  3:575987/1‑149 (MQ=255)

             gTTCATTCACTAATTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCcg                                                                                                                                       >  4:222167/1‑149 (MQ=255)

                      cTAATTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAg                                                                                                                              >  2:228353/1‑149 (MQ=255)

                        aaTTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAACATCACGCTg                                                                                                                                            <  4:577959/133‑1 (MQ=255)

                        aaTTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAACATCACGCTg                                                                                                                                            >  3:577959/1‑133 (MQ=255)

                         aTTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAg                                                                                                                              <  3:489007/146‑1 (MQ=255)

                         aTTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAg                                                                                                                              >  4:489007/1‑146 (MQ=255)

                           tGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAAt                                                                                                                         <  3:222167/149‑1 (MQ=255)

                             gatgatCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCGTGATGCTGGcc                                                                                                                                         <  2:162670/131‑1 (MQ=255)

                             gatgatCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCGTGATGCTGGcc                                                                                                                                         >  1:162670/1‑131 (MQ=255)

                                 atCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCaa                                                                                                                   >  1:470108/1‑149 (MQ=255)

                                   cTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGc                                                                                                                     <  1:96086/145‑1 (MQ=255)

                                   cTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGc                                                                                                                     >  2:96086/1‑145 (MQ=255)

                                   cTTATTCCTTCGCTCGAAAGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGTCCGCGGTTTCAGGGAATGAGCAaca                                                                                                                 <  1:687964/149‑1 (MQ=255)

                                    ttATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAacac                                                                                                                <  2:186068/149‑1 (MQ=255)

                                    ttATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAacac                                                                                                                >  1:186068/1‑149 (MQ=255)

                                       ttCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACttt                                                                                                             <  3:335/149‑1 (MQ=255)

                                           ttCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGccc                                                                                                         >  4:669350/1‑149 (MQ=255)

                                                 cGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATa                                                                                                   >  1:403827/1‑149 (MQ=255)

                                                  gaatgaatTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAg                                                                                                  >  4:71369/1‑149 (MQ=255)

                                                  gaatgaatTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAg                                                                                                  >  1:512266/1‑149 (MQ=255)

                                                                     tACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCa                                                                                                <  3:41870/132‑1 (MQ=255)

                                                                     tACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCa                                                                                                >  4:41870/1‑132 (MQ=255)

                                                                             ttCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCt                                                                       >  3:461872/1‑149 (MQ=255)

                                                                               cAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTgg                                                                     <  3:669350/149‑1 (MQ=255)

                                                                                aaTTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGAt                                                                                     <  3:210051/132‑1 (MQ=255)

                                                                                aaTTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGAt                                                                                     >  4:210051/1‑132 (MQ=255)

                                                                                             gtAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCaaa                                                       <  4:575987/149‑1 (MQ=255)

                                                                                               aaaCGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGc                                                     <  2:65407/149‑1 (MQ=255)

                                                                                                   gAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTcc                                                 >  3:133183/1‑149 (MQ=255)

                                                                                                             cATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCg                                       >  2:495477/1‑149 (MQ=255)

                                                                                                                    gAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATg                                <  1:495477/149‑1 (MQ=255)

                                                                                                                     aaTGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGa                                          <  2:549072/138‑1 (MQ=255)

                                                                                                                     aaTGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGa                                          >  1:549072/1‑138 (MQ=255)

                                                                                                                     aaTGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATgg                               >  4:127532/1‑149 (MQ=255)

                                                                                                                          tCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCa                          >  2:512029/1‑149 (MQ=255)

                                                                                                                            tGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAg                         >  1:591220/1‑148 (MQ=255)

                                                                                                                            tGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAg                         <  2:591220/148‑1 (MQ=255)

                                                                                                                              ttttGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGTTGAGCGATTaa                                  <  3:543887/137‑1 (MQ=255)

                                                                                                                              ttttGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTaa                                  >  4:543887/1‑137 (MQ=255)

                                                                                                                                  gCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGAGGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAAc                  <  2:512266/149‑1 (MQ=255)

                                                                                                                                    acaATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACtt                >  4:443850/1‑149 (MQ=255)

                                                                                                                                           cGGGCCAGCGTGATGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACTTACg             >  3:624585/1‑145 (MQ=255)

                                                                                                                                           cGGGCCAGCGTGATGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACTTACg             <  4:624585/145‑1 (MQ=255)

                                                                                                                                           cGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTACAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACTTACGTTCt         <  4:461872/149‑1 (MQ=255)

                                                                                                                                            gggCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGCCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACTTACGTTCTg        >  1:654343/1‑149 (MQ=255)

                                                                                                                                              gCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACTTACGTTCTGTc      <  2:403827/149‑1 (MQ=255)

                                                                                                                                                  gCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACTTACGTTCTGTCAGCa  >  2:488882/1‑149 (MQ=255)

AGCACGGTTCCCTGTTCATTCACTAATTGGATGATCTTATTCCTTCGCTCGAATGAATTCATCGTCATTTACCCATATTCAATTGTGGCTAGTGTAAACGAAGGGGGACCATTGGTGAATGATCTGTTTTGCACAATACCGGGCCAGCATCACGCTGGCCCGCGGTTTCAGGGAATGAGCAACACTTTGCCCGGCATAGCATTACGAGCGATGTCACGCACCGCCTGGGCGAAGCTTTCAAAGCTTCCACGGTGAGCGATTAATGGCTCCAGGCTTAACTTACGTTCTGTCAGCA  >  NC_000913/2171666‑2171960

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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