BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714241.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 249,342 number of mapped reads = 69,042 (27.69%) number of supplementary alignments = 2,809 (1.13%) number of secondary alignments = 0 number of mapped bases = 8,175,565 bp number of sequenced bases = 8,038,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,615 duplication rate = 41.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7329 >>>>>>> ACTG content number of A's = 1,847,242 bp (22.98%) number of C's = 1,418,808 bp (17.65%) number of T's = 1,731,915 bp (21.54%) number of G's = 3,040,644 bp (37.82%) number of N's = 204 bp (0%) GC percentage = 55.47% >>>>>>> Mismatches and indels general error rate = 0.0413 number of mismatches = 295,870 number of insertions = 8,595 mapped reads with insertion percentage = 11.51% number of deletions = 23,857 mapped reads with deletion percentage = 32.35% homopolymer indels = 32.11% >>>>>>> Coverage mean coverageData = 0.0026X std coverageData = 2.0224X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 531375 0.00213189037551084 0.4390132914553639 chr2 243199373 1979821 0.008140732336509766 6.96607418302466 chr3 198022430 345207 0.0017432722141628098 0.5859407356792956 chr4 191154276 217698 0.0011388602157139294 0.21945561154694795 chr5 180915260 294601 0.001628392209700829 0.3241073919751609 chr6 171115067 268095 0.001566752739546892 0.42403890428599283 chr7 159138663 328746 0.002065783347695965 0.45650451335867726 chr8 146364022 324240 0.002215298510996097 0.4872622531819107 chr9 141213431 214879 0.0015216612079909028 0.32619211707761947 chr10 135534747 286100 0.0021108978054166436 0.7050481128689471 chr11 135006516 220385 0.0016324026908449366 0.29685268589707164 chr12 133851895 382617 0.0028585101466064413 0.6300729589797137 chr13 115169878 175147 0.0015207709085182845 0.3705576148143954 chr14 107349540 327345 0.003049337705592404 0.9237696490973831 chr15 102531392 215874 0.002105442984720231 0.397727460535918 chr16 90354753 185101 0.002048602800120543 0.39021416755516747 chr17 81195210 430557 0.005302738917726797 1.5947674976674375 chr18 78077248 182558 0.0023381715503087404 0.5086596504215604 chr19 59128983 223069 0.0037725830664126253 0.5427724525425396 chr20 63025520 149156 0.00236659689598753 0.43219688599131406 chr21 48129895 36339 7.550193076465261E-4 0.11007745157747643 chr22 51304566 61151 0.0011919212024910219 0.19589052970661 chrMT 16571 105847 6.38748415907308 51.634886893553585 chrX 155270560 662496 0.004266719975763596 0.4307203389855299 chrY 59373566 27161 4.5745946942112254E-4 0.114140919390522