BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173870.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,459,988 number of mapped reads = 1,424,383 (97.56%) number of supplementary alignments = 143,906 (9.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 712,772 number of mapped paired reads (second in pair) = 711,611 number of mapped paired reads (both in pair) = 1,400,288 number of mapped paired reads (singletons) = 24,095 number of mapped bases = 168,714,902 bp number of sequenced bases = 168,619,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,102,388 duplication rate = 64.58% >>>>>>> Insert size mean insert size = 1,191,632.4264 std insert size = 9,881,324.8586 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.8538 >>>>>>> ACTG content number of A's = 50,833,698 bp (30.15%) number of C's = 32,921,748 bp (19.52%) number of T's = 50,725,407 bp (30.08%) number of G's = 34,136,833 bp (20.24%) number of N's = 1,725 bp (0%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,710,582 number of insertions = 19,124 mapped reads with insertion percentage = 1.29% number of deletions = 37,811 mapped reads with deletion percentage = 2.59% homopolymer indels = 42.96% >>>>>>> Coverage mean coverageData = 0.0545X std coverageData = 0.965X There is a 1.2% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 13284621 0.05329824634619466 0.7319853515859955 chr2 243199373 15107724 0.06212073581291675 2.4230514076076037 chr3 198022430 11880567 0.05999606711219532 0.6948121449110995 chr4 191154276 11698615 0.061199860368281796 0.7777696806688145 chr5 180915260 10280036 0.056822381926212306 0.6838217076971332 chr6 171115067 10186972 0.05953287561755155 0.7258896319259052 chr7 159138663 9669641 0.06076236168956629 0.7661557666940801 chr8 146364022 8650350 0.05910161446642946 0.8196803498506333 chr9 141213431 7455489 0.05279589163158283 0.79629090013405 chr10 135534747 8377781 0.06181279107711028 0.8745895350545221 chr11 135006516 7441892 0.055122465348265114 0.6679227238821481 chr12 133851895 7843617 0.058599222670698836 0.6971248465572487 chr13 115169878 5584514 0.048489362817593674 0.6263878400855749 chr14 107349540 5412583 0.05042017879163711 0.641057328894464 chr15 102531392 4994135 0.048708350706874244 0.6188004649038447 chr16 90354753 4836510 0.053528008648310955 0.711759560065335 chr17 81195210 4300254 0.05296191733477874 0.6549966706942995 chr18 78077248 4646353 0.0595096922473497 0.9053575622962332 chr19 59128983 2919626 0.04937724026134527 0.656281704946725 chr20 63025520 3664148 0.05813752905172381 0.6991825128038723 chr21 48129895 2384168 0.049536114716227826 0.6813436870203448 chr22 51304566 1979456 0.03858245287563684 0.5579031994988743 chrMT 16571 169962 10.256592842918351 13.404554619982743 chrX 155270560 4585408 0.02953172835855039 0.4897224910551583 chrY 59373566 1360480 0.02291390077530462 0.5068197921179179