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
A1 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,824,380	2 bp→AA	100%	pseudogene (513‑514/687 nt)	rph →	ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,824,380	0	G	A	100.0%	142.4 / NA	49	pseudogene (513/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (24/25); total (24/25)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*	W3110S.gb	3,824,381	0	G	A	100.0%	143.6 / NA	49	pseudogene (514/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (24/25); total (24/25)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATG  >  W3110S.gb/3824319‑3824440

||

aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                        >  1:2665610/1‑68 (MQ=255)

aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                       >  1:1076050/1‑69 (MQ=255)

aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                       >  1:3133106/1‑69 (MQ=255)

      acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                 <  1:1211448/67‑1 (MQ=255)

      acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                 <  1:3128159/67‑1 (MQ=255)

         cGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAAt                                              >  1:385139/1‑69 (MQ=255)

             gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                       <  1:2746670/56‑1 (MQ=255)

               aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                       <  1:2433668/54‑1 (MQ=255)

               aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                       <  1:2244614/54‑1 (MQ=255)

                aGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                          >  1:3158052/1‑66 (MQ=255)

                aGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                        <  1:2272051/68‑1 (MQ=255)

                 gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                      <  1:1900428/69‑1 (MQ=255)

                 gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                      <  1:75732/69‑1 (MQ=255)

                 gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                      >  1:401819/1‑69 (MQ=255)

                 gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                      >  1:64447/1‑69 (MQ=255)

                 gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                      >  1:3468036/1‑69 (MQ=255)

                             gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                          <  1:525453/69‑1 (MQ=255)

                                  ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagat                       <  1:885086/67‑2 (MQ=255)

                                  ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                       <  1:770426/67‑1 (MQ=255)

                                  ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                       <  1:3194085/67‑1 (MQ=255)

                                  ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                       <  1:2285045/67‑1 (MQ=255)

                                  ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                       <  1:2743509/67‑1 (MQ=255)

                                   tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                 <  1:1742436/40‑1 (MQ=16)

                                   tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                 <  1:1338804/40‑1 (MQ=16)

                                   tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                 <  1:1840713/40‑1 (MQ=16)

                                   tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                             >  1:55162/1‑60 (MQ=255)

                                   tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                             >  1:1914151/1‑60 (MQ=255)

                                   tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                             >  1:1230306/1‑60 (MQ=255)

                                   tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                              <  1:2779168/59‑1 (MQ=255)

                                   tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                              <  1:2080452/59‑1 (MQ=255)

                                         ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg              <  1:629499/66‑1 (MQ=255)

                                           taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa            <  1:2159290/68‑1 (MQ=255)

                                            aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                   >  1:1576728/1‑61 (MQ=255)

                                            aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                   >  1:153409/1‑61 (MQ=255)

                                             ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                      >  1:3209804/1‑41 (MQ=25)

                                             ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa            >  1:3465008/1‑67 (MQ=255)

                                             ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa            >  1:1524557/1‑67 (MQ=255)

                                             ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa             >  1:3131117/1‑66 (MQ=255)

                                               gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt         >  1:336393/4‑68 (MQ=255)

                                               gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt         <  1:1199541/65‑1 (MQ=255)

                                                taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa            >  1:657729/3‑64 (MQ=255)

                                                taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa            >  1:920554/3‑64 (MQ=255)

                                                taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa            >  1:369341/3‑64 (MQ=255)

                                                taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa            <  1:1097882/62‑1 (MQ=255)

                                                  aaCGGTGAAGGAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg     >  1:1949320/1‑69 (MQ=255)

                                                  aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg     >  1:6194/1‑69 (MQ=255)

                                                  aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg     >  1:1481256/1‑69 (MQ=255)

                                                     ggtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg  <  1:3360150/66‑1 (MQ=255)

                                                     ggtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg  <  1:1899764/66‑1 (MQ=255)

||

AAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATG  >  W3110S.gb/3824319‑3824440

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A