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 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

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%	158.1 / NA	42	G154G (GGT→GGC)	gspD	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/23); total (19/23)

GGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATC  >  NC_000913/3456708‑3456965

ggATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                         <  1:415324/139‑1 (MQ=255)

 gatgatTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTtgtg                                                                                                                        <  2:518413/139‑1 (MQ=255)

              aGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCt                                                                                                           <  1:565199/139‑1 (MQ=255)

               gTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTc                                                                                                          >  2:184521/1‑139 (MQ=255)

                  ctcGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                       <  2:482428/139‑1 (MQ=255)

                          ggCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTtgtg                                                                                                                        <  2:67120/114‑1 (MQ=255)

                          ggCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTtgtg                                                                                                                        >  1:67120/1‑114 (MQ=255)

                          ggCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGa                                                                                                                >  2:578889/1‑122 (MQ=255)

                          ggCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGa                                                                                                                <  1:578889/122‑1 (MQ=255)

                          ggCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTa                                                                                               >  2:612191/1‑139 (MQ=255)

                          ggCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTa                                                                                               >  2:580765/1‑139 (MQ=255)

                                     tgaGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                       <  2:185793/120‑1 (MQ=255)

                                     tgaGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                       >  1:185793/1‑120 (MQ=255)

                                     tgaGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGt                                                                                    >  1:214250/1‑139 (MQ=255)

                                           ggTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTc                                                                                                  >  2:917/1‑119 (MQ=255)

                                           ggTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTc                                                                                                  <  1:917/119‑1 (MQ=255)

                                           ggTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGcc                                                                              >  2:579339/1‑139 (MQ=255)

                                            gTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCt                                                                             <  1:184521/139‑1 (MQ=255)

                                             tCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTCGCGTCGGCAATATTGTGCATTATGAAACCTCCTACGTTCTTATTCTGACCGGTCGTGCCTc                                                                            <  1:425281/139‑1 (MQ=255)

                                                cccGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                         <  1:568052/139‑1 (MQ=255)

                                                cccGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                         <  2:214250/139‑1 (MQ=255)

                                                 ccGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccacc                                                                        >  1:534286/1‑139 (MQ=255)

                                                              cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                         <  1:589562/77‑1 (MQ=255)

                                                              cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                         >  2:589562/1‑77 (MQ=255)

                                                                 gagaACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                        <  1:580765/139‑1 (MQ=255)

                                                                         tCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGt                                                                                 <  2:79386/106‑1 (MQ=255)

                                                                         tCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGt                                                                                 >  1:79386/1‑106 (MQ=255)

                                                                                   gACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTg                                      >  1:599294/1‑139 (MQ=255)

                                                                                     ccTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGAt                                    <  1:612191/139‑1 (MQ=255)

                                                                                        ggCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                         >  2:316533/1‑99 (MQ=255)

                                                                                        ggCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                         <  1:316533/99‑1 (MQ=255)

                                                                                         gCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                         >  2:166883/1‑50 (MQ=255)

                                                                                         gCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                         <  1:166883/50‑1 (MQ=255)

                                                                                          ccccccTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCAt                               <  1:579339/139‑1 (MQ=255)

                                                                                             cccTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCgg                            >  1:156335/1‑139 (MQ=255)

                                                                                                     cGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                        >  2:254275/1‑103 (MQ=255)

                                                                                                     cGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                        <  1:254275/103‑1 (MQ=255)

                                                                                                                  atgCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAattat       <  2:534286/139‑1 (MQ=255)

                                                                                                                    gCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTAtt                                                                                             >  2:396503/1‑51 (MQ=255)

                                                                                                                    gCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTAtt                                                                                             <  1:396503/51‑1 (MQ=255)

                                                                                                                    gCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTc     <  2:156335/139‑1 (MQ=255)

                                                                                                                       ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTAATc  >  1:425847/1‑139 (MQ=255)

GGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATC  >  NC_000913/3456708‑3456965

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