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
A2 F1 I2 R1	78	65.3	3016648	94.6%	2853749	111.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,456,838	T→C	G154G (GGT→GGC)	gspD →	general secretory pathway component, cryptic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,456,838	0	T	C	100.0%	231.6 / NA	61	G154G (GGT→GGC)	gspD	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (29/32); total (29/32)

AGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATA  >  NC_000913/3456706‑3456972

aGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgtt                                                                                                                                  <  2:1292841/139‑1 (MQ=255)

  ggATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                                <  2:1441703/139‑1 (MQ=255)

  ggATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                                <  1:1198099/139‑1 (MQ=255)

        ttGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTa                                                                                                                          >  1:692637/1‑139 (MQ=255)

              aCAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAAcc                                                                                                                    >  1:681779/1‑139 (MQ=255)

                 gTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTc                                                                                                                 >  2:966276/1‑139 (MQ=255)

                 gTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTc                                                                                                                 >  1:499481/1‑139 (MQ=255)

                  ttCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTcc                                                                                                                >  1:277104/1‑139 (MQ=255)

                   tctcGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCa                                                                                                               >  2:1469148/1‑139 (MQ=255)

                    ctcGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  2:681779/139‑1 (MQ=255)

                        tCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGtt                                                                                                          <  1:1071426/139‑1 (MQ=255)

                                   gTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGAc                                                                                               <  1:144615/139‑1 (MQ=255)

                                   gTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGAc                                                                                               <  2:692637/139‑1 (MQ=255)

                                       tgaGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGt                                                                                           <  2:277104/139‑1 (MQ=255)

                                       tgaGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGt                                                                                           <  2:346332/139‑1 (MQ=255)

                                          gTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGt                                                                                        <  1:1187506/139‑1 (MQ=255)

                                           ttGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATg                                                                                                                        >  2:599818/1‑106 (MQ=255)

                                           ttGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATg                                                                                                                        <  1:599818/106‑1 (MQ=255)

                                              gTCACCCGAATTGTACCACTTGAGAACGTTCCTGCTCGTGACCTGGTCCCCCTGCTCCGCCAGATGATGGACGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCt                                                                                    >  2:865186/1‑139 (MQ=255)

                                               tCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTc                                                                                   <  1:1049002/139‑1 (MQ=255)

                                                   ccGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccacc                                                                               <  1:775129/139‑1 (MQ=255)

                                                             ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  2:949130/98‑1 (MQ=255)

                                                             ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              >  1:949130/1‑98 (MQ=255)

                                                             ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCt                                                                                    >  1:1176936/1‑124 (MQ=255)

                                                             ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCt                                                                                    <  2:1176936/124‑1 (MQ=255)

                                                             ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAAc                                                                     >  2:596531/1‑139 (MQ=255)

                                                                cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              >  1:1436452/1‑95 (MQ=255)

                                                                cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  1:1380666/95‑1 (MQ=255)

                                                                cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  2:1436452/95‑1 (MQ=255)

                                                                cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              >  2:1380666/1‑95 (MQ=255)

                                                                  tGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                <  1:482188/123‑1 (MQ=255)

                                                                  tGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                >  2:482188/1‑123 (MQ=255)

                                                                     gaACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGaa                                                             <  1:596531/139‑1 (MQ=255)

                                                                                cTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAgcg                                                  >  1:393597/1‑139 (MQ=255)

                                                                                           gCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                <  2:990708/98‑1 (MQ=255)

                                                                                           gCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                >  1:990708/1‑98 (MQ=255)

                                                                                           gCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCa                                       <  1:963122/139‑1 (MQ=255)

                                                                                              ccccTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCg                                    <  2:393597/139‑1 (MQ=255)

                                                                                                      ccGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACagag                            >  1:848577/1‑139 (MQ=255)

                                                                                                         ccAGATGATGGATGCGGGTAGCGTCGGCAGTGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGt                                                                                           >  1:1006603/1‑73 (MQ=255)

                                                                                                         ccAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCCTATTCTGACCGGt                                                                                           <  2:1006603/73‑1 (MQ=255)

                                                                                                             atgatgGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              >  2:1405333/1‑50 (MQ=255)

                                                                                                             atgatgGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  1:1405333/50‑1 (MQ=255)

                                                                                                             atgatgGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                <  1:746506/80‑1 (MQ=255)

                                                                                                             atgatgGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                >  2:746506/1‑80 (MQ=255)

                                                                                                                   gatgCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAatta               <  1:865186/139‑1 (MQ=255)

                                                                                                                    atgCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATaaa                                                     >  2:1314580/1‑100 (MQ=255)

                                                                                                                    atgCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATaaa                                                     <  1:1314580/100‑1 (MQ=255)

                                                                                                                       cGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                >  1:743438/1‑70 (MQ=255)

                                                                                                                       cGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                <  2:743438/70‑1 (MQ=255)

                                                                                                                       cGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCa           >  2:1320029/1‑139 (MQ=255)

                                                                                                                         ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATaaa                                                                      >  1:1507816/1‑78 (MQ=255)

                                                                                                                         ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATaaa                                                                      <  2:1507816/78‑1 (MQ=255)

                                                                                                                         ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                               <  2:6980/85‑1 (MQ=255)

                                                                                                                         ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                               >  1:6980/1‑85 (MQ=255)

                                                                                                                         ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                               >  2:749648/1‑85 (MQ=255)

                                                                                                                         ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                               <  1:749648/85‑1 (MQ=255)

                                                                                                                          gTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCgg                                   <  2:700297/112‑1 (MQ=255)

                                                                                                                          gTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCgg                                   >  1:700297/1‑112 (MQ=255)

                                                                                                                             gCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGa     >  2:922212/1‑139 (MQ=255)

                                                                                                                                tCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAata  >  1:1209707/1‑139 (MQ=255)

AGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATA  >  NC_000913/3456706‑3456972

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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