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 F1 I1 R1	770	51.4	2439994	93.8%	2288714	110.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,787,434	G→A	pseudogene (1038/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,787,434	0	G	A	100.0%	205.9 / NA	63	pseudogene (1038/2253 nt)	ygaQ	uncharacterized protein, putative enzyme
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (34/29); total (34/29)

CGATATCATTCCTGATTATACCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAGCAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTAAGGATGAATGGGAA  >  NC_000913/2787302‑2787569

cGATATCATTCCTGATTATACCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGt                                                                                                                                   <  2:234737/139‑1 (MQ=255)

              aTTATACCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTcc                                                                                                                     >  1:760136/1‑139 (MQ=255)

                   aCCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCcattca                                                                                                                >  1:676210/1‑139 (MQ=255)

                       ttAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGAtt                                                                                                                       >  2:947052/1‑128 (MQ=255)

                       ttAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGAtt                                                                                                                       <  1:947052/128‑1 (MQ=255)

                       ttAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCcat                                                                                                                   <  1:1104208/132‑1 (MQ=255)

                       ttAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCcat                                                                                                                   >  2:1104208/1‑132 (MQ=255)

                       ttAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTaa                                                                                                            >  2:866710/1‑139 (MQ=255)

                        tAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTc                                                                                                                                  >  1:679445/1‑116 (MQ=255)

                        tAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTc                                                                                                                                  <  2:679445/116‑1 (MQ=255)

                        tAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTaaa                                                                                                           <  2:959701/139‑1 (MQ=255)

                                 gggAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTa                                                                                                  >  2:619168/1‑139 (MQ=255)

                                    aaTTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCcattc                                                                                                                 <  1:912201/121‑1 (MQ=255)

                                    aaTTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCcattc                                                                                                                 >  2:912201/1‑121 (MQ=255)

                                     aTTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACaa                                                                                              >  2:943585/1‑139 (MQ=255)

                                      ttGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACaaa                                                                                             >  2:641599/1‑139 (MQ=255)

                                      ttGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACaaa                                                                                             >  2:1096168/1‑139 (MQ=255)

                                            gTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACg                                                                                       <  2:676210/139‑1 (MQ=255)

                                                tGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATcc                                                                                                      >  2:553774/1‑120 (MQ=255)

                                                tGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATcc                                                                                                      <  1:553774/120‑1 (MQ=255)

                                                tGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTaaa                                                                                   >  1:1081176/1‑139 (MQ=255)

                                                      aaaTGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAatc                                                                             <  1:866710/139‑1 (MQ=255)

                                                      aaaTGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAatc                                                                             <  1:943585/139‑1 (MQ=255)

                                                           aCCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAatccatcc                                                                        <  2:1081176/139‑1 (MQ=255)

                                                            ccTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAAtccatcca                                                                       >  1:673833/1‑139 (MQ=255)

                                                            ccTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAAtccatcca                                                                       >  2:485814/1‑139 (MQ=255)

                                                             cTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCag                                                                      <  1:1096168/139‑1 (MQ=255)

                                                              tGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCaga                                                                     <  1:641599/139‑1 (MQ=255)

                                                                                atatACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTACCAAAAGACCGTAGACAAATCCATCCAGAAGATATACATCTCACTGc                                                   >  1:1131868/1‑139 (MQ=255)

                                                                                 tataCGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCa                                                  <  2:760136/139‑1 (MQ=255)

                                                                                       aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAg                                                                                                                                     <  2:298925/50‑1 (MQ=255)

                                                                                       aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAg                                                                                                                                     >  1:298925/1‑50 (MQ=255)

                                                                                       aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGt                                                                                                   <  2:288650/84‑1 (MQ=255)

                                                                                       aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGt                                                                                                   >  1:288650/1‑84 (MQ=255)

                                                                                       aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAat                                                                              >  2:406407/1‑105 (MQ=255)

                                                                                       aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAat                                                                              <  1:406407/105‑1 (MQ=255)

                                                                                       aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGAc                                            >  2:928347/1‑139 (MQ=255)

                                                                                       aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGAc                                            >  2:582701/1‑139 (MQ=255)

                                                                                           aaGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCca                                                                                                                    <  2:252352/63‑1 (MQ=255)

                                                                                           aaGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCca                                                                                                                    >  1:252352/1‑63 (MQ=255)

                                                                                            aGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGa                                       <  2:1131868/139‑1 (MQ=255)

                                                                                                  gTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAg                                 >  1:674155/1‑139 (MQ=255)

                                                                                                      aGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTc                                         <  2:817352/127‑1 (MQ=255)

                                                                                                      aGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTc                                         >  1:817352/1‑127 (MQ=255)

                                                                                                          ataGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATa                         <  1:928347/139‑1 (MQ=255)

                                                                                                           taGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATaa                        >  2:361876/1‑139 (MQ=255)

                                                                                                           taGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATaa                        >  2:175688/1‑139 (MQ=255)

                                                                                                            aGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                       <  2:192732/139‑1 (MQ=255)

                                                                                                            aGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                       <  1:485814/139‑1 (MQ=255)

                                                                                                            aGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                       >  1:372356/1‑139 (MQ=255)

                                                                                                                 gtggtATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCaa                                  >  2:406814/1‑123 (MQ=255)

                                                                                                                 gtggtATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCaa                                  <  1:406814/123‑1 (MQ=255)

                                                                                                                   ggtATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTa                >  1:844737/1‑139 (MQ=255)

                                                                                                                    gtATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAatccatcc                                                                        <  2:911263/82‑1 (MQ=255)

                                                                                                                    gtATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAatccatcc                                                                        >  1:911263/1‑82 (MQ=255)

                                                                                                                           tGGCTATGAACAAGGTCAGGTTTTCATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTAAGGATGaa        >  2:744988/1‑139 (MQ=255)

                                                                                                                            ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACAtct                                                         <  1:360823/89‑1 (MQ=255)

                                                                                                                            ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACAtct                                                         >  2:360823/1‑89 (MQ=255)

                                                                                                                            ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                       >  2:859344/1‑123 (MQ=255)

                                                                                                                            ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAACATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                       <  1:859344/123‑1 (MQ=255)

                                                                                                                                 ttAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAGAAGAACGTAAACAGATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTAAGGATGAATGGGaa  <  1:744988/139‑1 (MQ=255)

                                                                                                                                 ttAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAatccatcc                                                                        <  2:220189/69‑1 (MQ=255)

                                                                                                                                 ttAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAatccatcc                                                                        >  1:220189/1‑69 (MQ=255)

CGATATCATTCCTGATTATACCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAGCAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTAAGGATGAATGGGAA  >  NC_000913/2787302‑2787569

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