BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716637.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 = 688,796 number of mapped reads = 619,838 (89.99%) number of supplementary alignments = 2,368 (0.34%) number of secondary alignments = 0 number of mapped bases = 35,371,598 bp number of sequenced bases = 35,362,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,196 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8692 >>>>>>> ACTG content number of A's = 8,885,184 bp (25.13%) number of C's = 7,001,071 bp (19.8%) number of T's = 10,945,522 bp (30.95%) number of G's = 8,529,530 bp (24.12%) number of N's = 813 bp (0%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 173,241 number of insertions = 2,006 mapped reads with insertion percentage = 0.32% number of deletions = 5,664 mapped reads with deletion percentage = 0.91% homopolymer indels = 42.24% >>>>>>> Coverage mean coverageData = 0.0114X std coverageData = 0.1234X There is a 1.08% of reference with a coverageData >= 1X There is a 0.04% 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 3984508 0.01598595014132382 0.17303303317736438 chr2 243199373 2924780 0.012026264557844892 0.13375488145145806 chr3 198022430 2288577 0.011557160469144834 0.11129440777105175 chr4 191154276 2251429 0.011778072911118138 0.11589561348772667 chr5 180915260 1791426 0.009902017110110004 0.10399634152586587 chr6 171115067 1865158 0.010900022030204973 0.11239656251601444 chr7 159138663 1516416 0.009528897449641135 0.11050906643338419 chr8 146364022 2257980 0.015427151899392325 0.1386603621011951 chr9 141213431 1287326 0.009116172526110494 0.11581775027670373 chr10 135534747 1666912 0.012298779736535016 0.12482294000043949 chr11 135006516 1110126 0.008222758670403731 0.11315567858690931 chr12 133851895 1582770 0.01182478589488778 0.11377658835640092 chr13 115169878 1095959 0.009516021194361254 0.10098056741215752 chr14 107349540 1241655 0.011566467820914743 0.11547294911947505 chr15 102531392 1031298 0.010058363393720432 0.10445708272475555 chr16 90354753 1027745 0.011374553810135479 0.11473899920686197 chr17 81195210 789643 0.00972524118109923 0.10320889903607558 chr18 78077248 870997 0.011155580176186538 0.17339168375952863 chr19 59128983 668920 0.011312895403595898 0.133316782516761 chr20 63025520 1133799 0.01798952233952215 0.14116241899337892 chr21 48129895 463826 0.009636962640371437 0.10478287367062783 chr22 51304566 430444 0.008389974490769496 0.09468575775819071 chrMT 16571 2279 0.13752941886428097 0.4420132166450143 chrX 155270560 1989999 0.012816331698681321 0.12340277737272305 chrY 59373566 97626 0.0016442670800672474 0.05107721883942172