BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819122.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,156,945 number of mapped reads = 1,037,490 (89.67%) number of supplementary alignments = 3,507 (0.3%) number of secondary alignments = 0 number of mapped bases = 59,703,385 bp number of sequenced bases = 59,686,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,131 duplication rate = 1.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6318 >>>>>>> ACTG content number of A's = 14,420,186 bp (24.16%) number of C's = 10,836,897 bp (18.16%) number of T's = 18,415,049 bp (30.85%) number of G's = 16,013,091 bp (26.83%) number of N's = 892 bp (0%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 313,550 number of insertions = 4,012 mapped reads with insertion percentage = 0.38% number of deletions = 10,330 mapped reads with deletion percentage = 0.99% homopolymer indels = 41.75% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 0.2022X There is a 1.77% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 6344199 0.02545309205067136 0.3373877467799022 chr2 243199373 4143505 0.01703748224712734 0.22821873108798757 chr3 198022430 3754761 0.018961291405221115 0.14920410489783537 chr4 191154276 3070123 0.016060969517626693 0.1517720724908121 chr5 180915260 3133651 0.017321098286567978 0.14049787116765608 chr6 171115067 2629871 0.0153690206602321 0.16669758024910855 chr7 159138663 3109360 0.019538683694986177 0.2431242240161256 chr8 146364022 5377318 0.036739342951370935 0.22878351081641876 chr9 141213431 2593122 0.01836313997639502 0.184708384712492 chr10 135534747 3092079 0.022813920920219815 0.2326995331148361 chr11 135006516 2090690 0.01548584514246705 0.19059503504463007 chr12 133851895 2608075 0.019484782042122003 0.15007523226649294 chr13 115169878 1315480 0.011422083819520933 0.11402807149910521 chr14 107349540 1243696 0.011585480478071914 0.11823170630504372 chr15 102531392 1737691 0.016947892407429718 0.14622141542462064 chr16 90354753 1931989 0.021382261982388465 0.17249021800375225 chr17 81195210 2070769 0.025503585741080047 0.17671776481023221 chr18 78077248 1448642 0.01855395825426634 0.31190258941942794 chr19 59128983 1305907 0.022085734165256995 0.25319505750264054 chr20 63025520 1539917 0.024433229586999044 0.17066677352270027 chr21 48129895 847168 0.017601700564690615 0.15291634116365177 chr22 51304566 487859 0.009509075663947727 0.10498536507101526 chrMT 16571 12620 0.7615714199505159 0.9807148613966284 chrX 155270560 3584123 0.023083081557766005 0.17857845273456055 chrY 59373566 230770 0.003886746502643954 0.11943724177154816