BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237792.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,234,111 number of mapped reads = 3,665,729 (86.58%) number of supplementary alignments = 37,530 (0.89%) number of secondary alignments = 0 number of mapped bases = 257,147,578 bp number of sequenced bases = 257,040,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 743,058 duplication rate = 14.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3952 >>>>>>> ACTG content number of A's = 74,867,342 bp (29.13%) number of C's = 49,385,212 bp (19.21%) number of T's = 78,778,366 bp (30.65%) number of G's = 53,580,616 bp (20.85%) number of N's = 428,655 bp (0.17%) GC percentage = 40.06% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 2,128,813 number of insertions = 19,151 mapped reads with insertion percentage = 0.52% number of deletions = 60,085 mapped reads with deletion percentage = 1.62% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.0831X std coverageData = 1.2654X There is a 1.45% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% 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 18561812 0.07447047443865747 1.8661307839923584 chr2 243199373 22583798 0.09286125092107042 1.3850314229318266 chr3 198022430 14454165 0.07299256452917985 1.0140324616841392 chr4 191154276 18684550 0.09774591702044896 1.2234885169369907 chr5 180915260 13991984 0.07733998779318008 1.0669202564882567 chr6 171115067 14906991 0.08711676453365734 1.1417772300272035 chr7 159138663 13812153 0.08679319493842926 1.358984329730496 chr8 146364022 14880564 0.10166818181588369 1.4950237813554397 chr9 141213431 10528536 0.0745576106000852 1.1399706535615435 chr10 135534747 11560624 0.08529638528782586 1.2389737140732955 chr11 135006516 11192184 0.0829010653085811 1.1487672166271652 chr12 133851895 14313377 0.10693443675190403 1.2704135021584109 chr13 115169878 9349497 0.08118005473618718 1.08280673398114 chr14 107349540 6215879 0.05790317312957279 0.9077174119490875 chr15 102531392 7595130 0.0740761424559612 1.0373092197203082 chr16 90354753 5406820 0.059839906817076904 0.9497090938356317 chr17 81195210 5414961 0.06669064591371832 1.0022810996482765 chr18 78077248 9044061 0.11583478198411912 1.7633350241178538 chr19 59128983 4391142 0.07426378363382302 1.3049828353736832 chr20 63025520 7378229 0.11706732447427645 1.3844919637165862 chr21 48129895 3957857 0.08223282016301926 1.1222372503839335 chr22 51304566 3403031 0.06632998318317321 0.9841341477408599 chrMT 16571 121421 7.327318809969223 9.586557262643636 chrX 155270560 14676456 0.09452182049192068 1.1735544356042276 chrY 59373566 722356 0.01216628962457805 0.3708540651679952