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 F28 I1 R1	354	41.7	3110465	93.1%	2895842	61.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,410	T→A	pseudogene (543/687 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	3,824,410	0	T	A	100.0%	190.9 / NA	59	pseudogene (543/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (36/23); total (36/23)

GCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCG  >  W3110S.gb/3824348‑3824454

gctgTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:5040/4‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:2112518/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:2744166/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:2513316/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:2924726/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:2346688/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:778138/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:752554/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:3051156/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:1630998/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:1677756/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:454230/1‑65 (MQ=255)

gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                            >  1:405409/1‑65 (MQ=255)

                    aaaCGGTGAAGCATTTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:2308537/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:2343414/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:3022367/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:939163/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:2402396/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:2675516/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:188916/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:1760280/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:666524/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:846169/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:1288207/2‑63 (MQ=255)

                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                          >  1:125598/2‑63 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:332111/64‑1 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:821167/64‑1 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:866328/64‑1 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:1222828/64‑1 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:2597848/64‑1 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:1186184/64‑1 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:1699489/64‑1 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:1755263/64‑1 (MQ=255)

                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                        <  1:2341791/64‑1 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:1798565/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:1290353/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:1295806/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:1320493/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:1503753/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:1748284/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:384983/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:3073809/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:2339913/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:306879/1‑65 (MQ=255)

                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                      >  1:2348629/1‑65 (MQ=255)

                                           tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:2583542/64‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGTCATGAACGTAGTGATGACCGAAGACGGgcg  <  1:335478/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGTgcg  <  1:2824183/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:2587379/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:2664553/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:2703003/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:1436450/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:2569332/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:733926/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:1564509/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:2802466/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:341725/60‑1 (MQ=255)

                                               aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:2587438/60‑1 (MQ=255)

                                                         gACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg  <  1:2774549/50‑1 (MQ=255)

GCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCG  >  W3110S.gb/3824348‑3824454

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A