BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525026.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 = 1,028,534 number of mapped reads = 941,964 (91.58%) number of supplementary alignments = 3,511 (0.34%) number of secondary alignments = 0 number of mapped bases = 54,632,973 bp number of sequenced bases = 54,615,886 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,614 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4494 >>>>>>> ACTG content number of A's = 13,900,816 bp (25.45%) number of C's = 10,618,416 bp (19.44%) number of T's = 17,187,962 bp (31.47%) number of G's = 12,908,219 bp (23.63%) number of N's = 473 bp (0%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 272,700 number of insertions = 3,952 mapped reads with insertion percentage = 0.42% number of deletions = 10,254 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0176X std coverageData = 0.1825X There is a 1.63% of reference with a coverageData >= 1X There is a 0.09% 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 4463308 0.01790690824397184 0.30655474935961613 chr2 243199373 4669601 0.019200711508413303 0.20643431229589237 chr3 198022430 3592458 0.01814167213279829 0.14391772976589542 chr4 191154276 3421668 0.017900033792600068 0.15564342631565428 chr5 180915260 3171260 0.017528980142415846 0.14104111765730132 chr6 171115067 3091544 0.018067047246049933 0.1592515676147971 chr7 159138663 2990366 0.01879094585581632 0.20234806287314347 chr8 146364022 2865049 0.019574817368711007 0.19930810385281614 chr9 141213431 2237629 0.015845723626671176 0.15416962112182797 chr10 135534747 2669250 0.01969421169908555 0.197567264108728 chr11 135006516 2496532 0.018491937085466304 0.17200277988383 chr12 133851895 2436874 0.018205748973520324 0.1446998564640666 chr13 115169878 1747671 0.015174723029575494 0.13121002579712504 chr14 107349540 1568210 0.014608446389243959 0.13034492585145468 chr15 102531392 1592094 0.015527868772131758 0.13350203324152843 chr16 90354753 1590582 0.017603744653034468 0.14643430898162377 chr17 81195210 1525143 0.018783657311804477 0.15529980284222944 chr18 78077248 1516482 0.01942284133785043 0.2510855003906596 chr19 59128983 1157117 0.0195693709124001 0.21648686945738016 chr20 63025520 1180378 0.018728572172034438 0.14664643273058037 chr21 48129895 750373 0.015590580449011992 0.14491511149966593 chr22 51304566 678013 0.01321545142785147 0.12154777148438445 chrMT 16571 10227 0.6171625128236075 0.9288644403755093 chrX 155270560 3040693 0.01958319078645688 0.15766970434451041 chrY 59373566 170451 0.0028708230191193166 0.09819876076192384