BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068085.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,351,675 number of mapped reads = 3,021,362 (90.14%) number of supplementary alignments = 31,133 (0.93%) number of secondary alignments = 0 number of mapped bases = 201,518,039 bp number of sequenced bases = 201,421,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 194,386 duplication rate = 4.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.981 >>>>>>> ACTG content number of A's = 56,825,158 bp (28.21%) number of C's = 36,930,884 bp (18.34%) number of T's = 64,122,241 bp (31.83%) number of G's = 43,538,853 bp (21.62%) number of N's = 4,262 bp (0%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,590,507 number of insertions = 15,390 mapped reads with insertion percentage = 0.51% number of deletions = 59,279 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.0651X std coverageData = 0.7442X There is a 4.93% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 25006676 0.10032743709794006 1.835645328696401 chr2 243199373 16646990 0.06844997088047591 0.6262873147034068 chr3 198022430 12612282 0.06369117882252026 0.3157261154765755 chr4 191154276 12863422 0.067293404412256 0.334636412428048 chr5 180915260 9294450 0.05137460488407666 0.28825362161675405 chr6 171115067 10366068 0.06057951635550597 0.3625510092162487 chr7 159138663 12718439 0.0799204841880568 0.5783821625285186 chr8 146364022 8385206 0.05729007638229564 1.4039620609976808 chr9 141213431 5691655 0.04030533752841116 0.519741083041522 chr10 135534747 8913042 0.0657620440314099 0.47030020966670133 chr11 135006516 9725370 0.07203630082565793 0.4611138476280659 chr12 133851895 12531159 0.09361958603574495 0.41246427301719757 chr13 115169878 4629993 0.04020142315337002 0.2520630645355952 chr14 107349540 2601874 0.02423740241457951 0.2789594360606674 chr15 102531392 5985497 0.058377213878067706 0.3074433614456659 chr16 90354753 4400070 0.04869771488390876 0.31760224167653833 chr17 81195210 6077427 0.0748495754860416 0.37423230008227654 chr18 78077248 6612953 0.0846975677216492 1.0146976798548197 chr19 59128983 5559540 0.09402394084809475 1.0580468301506556 chr20 63025520 1640114 0.026023014169498322 0.27784780557480127 chr21 48129895 4410296 0.09163319388085098 0.387812562334887 chr22 51304566 1697378 0.033084345748095795 0.22134996576407676 chrMT 16571 110155 6.647456399734476 5.348289453191552 chrX 155270560 12560299 0.08089298447819085 0.42663524498011407 chrY 59373566 477684 0.008045398519603826 0.1385331299102914