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
A9 F1 I1 R1	759	71.0	3673240	91.5%	3361014	104.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,500,060	C→T	pseudogene (475/942 nt)	yjgX ←	pseudogene fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,500,060	0	C	T	100.0%	198.3 / NA	61	pseudogene (475/942 nt)	yjgX	pseudogene fragment
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (30/31); total (30/31)

ATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGCTAGGAGTTAAGGCTGTCACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAG  >  NC_000913/4499926‑4500195

aTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                                                                     <  2:1408166/139‑1 (MQ=255)

aTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                                                                     <  2:698689/139‑1 (MQ=255)

           aCCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                                          <  1:978416/139‑1 (MQ=255)

                cGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                                                                     <  2:1101424/139‑1 (MQ=255)

                   aGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCca                                                                                                                  <  2:251458/139‑1 (MQ=255)

                    ggATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                                                                     >  1:601117/1‑135 (MQ=255)

                    ggATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                                                                     <  2:601117/135‑1 (MQ=255)

                               aGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGa                                                                                                      >  2:711151/1‑139 (MQ=255)

                                gCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGaa                                                                                                     >  2:894778/1‑139 (MQ=255)

                                    gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAAtt                                                                                                 >  2:1149240/1‑139 (MQ=255)

                                    gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAAtt                                                                                                 >  1:541738/1‑139 (MQ=255)

                                    gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAAtt                                                                                                 >  1:447111/1‑139 (MQ=255)

                                         gAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCtt                                                                                            <  2:851348/139‑1 (MQ=255)

                                              ttATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGgag                                                                                       >  2:1412570/1‑139 (MQ=255)

                                                      tttACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTa                                                                               >  2:112441/1‑139 (MQ=255)

                                                          cTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCg                                                                           <  1:112441/139‑1 (MQ=255)

                                                             aTGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATccacca                                                                        >  1:379988/1‑139 (MQ=255)

                                                             aTGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCa                                                                        >  1:31293/1‑139 (MQ=255)

                                                                cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                                        <  1:439295/88‑1 (MQ=255)

                                                                cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                                        >  2:439295/1‑88 (MQ=255)

                                                                cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                                                                    <  2:888031/124‑1 (MQ=255)

                                                                cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                                                                    >  1:888031/1‑124 (MQ=255)

                                                                  ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                                          <  1:1598680/84‑1 (MQ=255)

                                                                  ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                                          >  2:1598680/1‑84 (MQ=255)

                                                                  ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCa                                                                   >  2:232822/1‑139 (MQ=255)

                                                                   gCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCAc                                                                  <  2:125198/139‑1 (MQ=255)

                                                                     gAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGt                                                                <  1:232822/139‑1 (MQ=255)

                                                                       ggTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCa                                                                   <  1:1558721/134‑1 (MQ=255)

                                                                       ggTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCa                                                                   >  2:1558721/1‑134 (MQ=255)

                                                                           aCAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGtt                                                          <  1:711151/139‑1 (MQ=255)

                                                                            cAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGttt                                                         <  2:1254187/139‑1 (MQ=255)

                                                                              ggCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTcc                                                       <  2:541738/139‑1 (MQ=255)

                                                                                 aaTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGt                                                    >  2:754870/1‑139 (MQ=255)

                                                                                 aaTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGt                                                    >  2:847613/1‑139 (MQ=255)

                                                                                 aaTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGATCTGTTTCCTGt                                                    >  2:872539/1‑139 (MQ=255)

                                                                                      ttCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTaacaa                                               >  2:484975/1‑139 (MQ=255)

                                                                                             aTACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                                                                    <  1:1263817/95‑1 (MQ=255)

                                                                                             aTACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                                                                    >  2:1263817/1‑95 (MQ=255)

                                                                                               aCTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtaca                                                                                                                                      >  2:1583234/1‑43 (MQ=255)

                                                                                               aCTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtaca                                                                                                                                      <  1:1583234/43‑1 (MQ=255)

                                                                                                       aGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                                          >  1:1803187/1‑47 (MQ=255)

                                                                                                       aGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                                          <  2:1803187/47‑1 (MQ=255)

                                                                                                        ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCAtgtg                                                                                                           >  1:1519133/1‑61 (MQ=255)

                                                                                                        ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCAtgtg                                                                                                           <  2:1519133/61‑1 (MQ=255)

                                                                                                           aaTTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGATCCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGtt                                                               <  2:809142/102‑1 (MQ=255)

                                                                                                           aaTTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGtt                                                               >  1:809142/1‑102 (MQ=255)

                                                                                                             ttattCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                                        <  2:455021/43‑1 (MQ=255)

                                                                                                             ttattCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                                        >  1:455021/1‑43 (MQ=255)

                                                                                                                  cGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGgaagcg                   >  2:1275922/1‑139 (MQ=255)

                                                                                                                     ttAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGgaagcgaag                <  2:447111/138‑1 (MQ=255)

                                                                                                                         gAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGc            <  1:1275922/139‑1 (MQ=255)

                                                                                                                         gAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGc            <  1:1412570/139‑1 (MQ=255)

                                                                                                                         gAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGc            <  2:31293/139‑1 (MQ=255)

                                                                                                                         gAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCACCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGc            <  2:379988/139‑1 (MQ=255)

                                                                                                                          aGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGcc           <  1:894778/139‑1 (MQ=255)

                                                                                                                              aaGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAgcg                                                                     >  1:950444/1‑77 (MQ=255)

                                                                                                                              aaGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAgcg                                                                     <  2:950444/77‑1 (MQ=255)

                                                                                                                              aaGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTTCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTc       >  2:473713/1‑139 (MQ=255)

                                                                                                                               aGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGAt                                                                                  >  2:126790/1‑63 (MQ=255)

                                                                                                                               aGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGAt                                                                                  <  1:126790/63‑1 (MQ=255)

                                                                                                                               aGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGgaag                     <  1:293192/124‑1 (MQ=255)

                                                                                                                               aGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGgaag                     >  2:293192/1‑124 (MQ=255)

                                                                                                                                   tGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAg  >  1:217548/1‑139 (MQ=255)

ATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGCTAGGAGTTAAGGCTGTCACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAG  >  NC_000913/4499926‑4500195

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