BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716684.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 = 647,873 number of mapped reads = 530,142 (81.83%) number of supplementary alignments = 2,341 (0.36%) number of secondary alignments = 0 number of mapped bases = 30,077,243 bp number of sequenced bases = 30,068,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,715 duplication rate = 1.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.944 >>>>>>> ACTG content number of A's = 7,304,531 bp (24.29%) number of C's = 5,321,732 bp (17.7%) number of T's = 9,522,968 bp (31.67%) number of G's = 7,918,598 bp (26.34%) number of N's = 229 bp (0%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 157,314 number of insertions = 2,204 mapped reads with insertion percentage = 0.41% number of deletions = 5,744 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0097X std coverageData = 0.116X There is a 0.93% 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 2532393 0.010160026843022389 0.1315317160316936 chr2 243199373 2336091 0.009605662100123917 0.15357816830052856 chr3 198022430 1724590 0.008709063917658216 0.09731572120273002 chr4 191154276 1816766 0.009504187078713321 0.10473758184483847 chr5 180915260 1697629 0.009383558910398162 0.0996613305868518 chr6 171115067 1596049 0.009327343453630533 0.1059244463900397 chr7 159138663 1702522 0.01069835555926469 0.14133367259798413 chr8 146364022 1558330 0.010646947102888441 0.11636417130297445 chr9 141213431 1000668 0.0070862098096037334 0.0943988359095921 chr10 135534747 1351488 0.009971524128790384 0.13462073515442918 chr11 135006516 1073999 0.007955164178890447 0.09977143051511406 chr12 133851895 1501376 0.011216695886150884 0.1093420441328799 chr13 115169878 898648 0.007802804132518053 0.0912728403447141 chr14 107349540 1012898 0.009435513184313599 0.10123989498883879 chr15 102531392 1118471 0.010908571298827193 0.10829590606811508 chr16 90354753 1054523 0.011670918960953831 0.11545884428872448 chr17 81195210 1353516 0.016669899615999514 0.13516824077240672 chr18 78077248 546975 0.007005561978823844 0.11891283566193193 chr19 59128983 822596 0.013911891567625982 0.14184242111857212 chr20 63025520 983356 0.015602505143948038 0.1321035058901483 chr21 48129895 371059 0.007709532713503739 0.09255211117228135 chr22 51304566 288287 0.005619129494244235 0.07731251627349807 chrMT 16571 4017 0.24241144167521575 0.5505478129225487 chrX 155270560 1636451 0.010539351439191049 0.10901273811714725 chrY 59373566 94545 0.0015923753004830467 0.05593005424822387