BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717071.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 = 1,038,023 number of mapped reads = 943,098 (90.86%) number of supplementary alignments = 3,855 (0.37%) number of secondary alignments = 0 number of mapped bases = 54,705,570 bp number of sequenced bases = 54,687,512 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,728 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8269 >>>>>>> ACTG content number of A's = 13,338,379 bp (24.39%) number of C's = 10,235,521 bp (18.72%) number of T's = 17,610,412 bp (32.2%) number of G's = 13,502,254 bp (24.69%) number of N's = 946 bp (0%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 277,168 number of insertions = 4,149 mapped reads with insertion percentage = 0.44% number of deletions = 11,253 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.46% >>>>>>> Coverage mean coverageData = 0.0177X std coverageData = 0.187X There is a 1.63% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 4386960 0.017600598074337396 0.2701298110337708 chr2 243199373 4618481 0.018990513598075763 0.2750042907689131 chr3 198022430 3605422 0.018207139463948606 0.14422072962946825 chr4 191154276 3514456 0.018385442761426903 0.1643442148783838 chr5 180915260 3268380 0.01806580605748791 0.1431937335008482 chr6 171115067 3134629 0.018318836879513363 0.1573801454464804 chr7 159138663 2956777 0.01857987835426266 0.20454083591393515 chr8 146364022 2753775 0.018814562228960885 0.21647337295771196 chr9 141213431 2312364 0.016374957988238386 0.1565697646900949 chr10 135534747 2660335 0.019628435208574227 0.20807862599246116 chr11 135006516 2455462 0.018187729546327972 0.1632725322850121 chr12 133851895 2478502 0.018516749426670427 0.14657330551797532 chr13 115169878 1684896 0.014629658633484009 0.12975153434330738 chr14 107349540 1663271 0.015493974170732358 0.13619752143070726 chr15 102531392 1604052 0.015644496467969535 0.13617178323139806 chr16 90354753 1623230 0.017965075949020633 0.15084389839906057 chr17 81195210 1553247 0.01912978610437734 0.15319471693511105 chr18 78077248 1445725 0.01851659781861164 0.2326106810564831 chr19 59128983 1188029 0.020092160218619013 0.22294422591248167 chr20 63025520 1189743 0.01887716277469825 0.15038618980532167 chr21 48129895 717021 0.01489762236132034 0.14579775739941825 chr22 51304566 680439 0.013262737667442698 0.1238444716770784 chrMT 16571 3939 0.2377044233902601 0.5002372423863637 chrX 155270560 3008200 0.019373923814018576 0.15823804092368332 chrY 59373566 198235 0.0033387753735391267 0.13405013779716907