BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524505.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 522,516 number of mapped reads = 483,924 (92.61%) number of supplementary alignments = 1,220 (0.23%) number of secondary alignments = 0 number of mapped bases = 28,404,166 bp number of sequenced bases = 28,395,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,302 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4533 >>>>>>> ACTG content number of A's = 7,360,344 bp (25.92%) number of C's = 5,543,394 bp (19.52%) number of T's = 8,808,917 bp (31.02%) number of G's = 6,681,973 bp (23.53%) number of N's = 466 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 130,540 number of insertions = 2,030 mapped reads with insertion percentage = 0.42% number of deletions = 5,227 mapped reads with deletion percentage = 1.07% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 0.1173X There is a 0.87% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 2472252 0.00991873958059266 0.17878195226164334 chr2 243199373 2293617 0.009431015268283606 0.12527924372180602 chr3 198022430 1619024 0.008175962692711123 0.09376198417307338 chr4 191154276 1669128 0.008731837105229076 0.10107317628640279 chr5 180915260 1600181 0.008844919991823796 0.09737568924660088 chr6 171115067 1262613 0.007378736555092486 0.09843845553416557 chr7 159138663 1472374 0.009252145093112916 0.13223020752776254 chr8 146364022 2264298 0.015470318245285716 0.13636424002621203 chr9 141213431 1260671 0.008927415693199891 0.10998015810718284 chr10 135534747 1541554 0.011373865625764586 0.12938384491259605 chr11 135006516 1002747 0.007427397059857467 0.10955751823557373 chr12 133851895 1366927 0.010212234948186577 0.10454170385461653 chr13 115169878 657327 0.005707455902662326 0.07827351643700724 chr14 107349540 712573 0.0066378766038494436 0.08507515599212014 chr15 102531392 766526 0.007476012809813408 0.08979462088002892 chr16 90354753 925039 0.010237856551940329 0.10848284442288937 chr17 81195210 1009758 0.012436176961670523 0.11725269426731687 chr18 78077248 713407 0.009137194487182745 0.15032835012862739 chr19 59128983 588869 0.009959058487442614 0.13705147117181138 chr20 63025520 837013 0.01328054096181991 0.11992044811755288 chr21 48129895 236133 0.0049061607136271545 0.07514111920234869 chr22 51304566 236341 0.004606627020292892 0.06999118688089255 chrMT 16571 35131 2.120028966266369 1.8253418063202191 chrX 155270560 1772687 0.011416761812413119 0.11501766759043983 chrY 59373566 87976 0.0014817368389158233 0.05021645013176333