BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818986.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 = 2,479,058 number of mapped reads = 2,445,135 (98.63%) number of supplementary alignments = 39,340 (1.59%) number of secondary alignments = 0 number of mapped bases = 226,096,036 bp number of sequenced bases = 225,960,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,199,510 duplication rate = 41.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0139 >>>>>>> ACTG content number of A's = 64,463,933 bp (28.53%) number of C's = 49,012,323 bp (21.69%) number of T's = 63,905,498 bp (28.28%) number of G's = 48,568,723 bp (21.49%) number of N's = 10,213 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,429,888 number of insertions = 35,399 mapped reads with insertion percentage = 1.4% number of deletions = 72,810 mapped reads with deletion percentage = 2.91% homopolymer indels = 40.93% >>>>>>> Coverage mean coverageData = 0.073X std coverageData = 0.8638X There is a 3.04% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 22414944 0.08992934063743015 1.5063715039437562 chr2 243199373 17590519 0.07232962315244126 1.2414408132372643 chr3 198022430 12666046 0.063962683419247 0.49329630706413735 chr4 191154276 12126277 0.06343712133334647 0.5758623983040825 chr5 180915260 11997763 0.06631703152072413 0.5223107252148633 chr6 171115067 9392200 0.05488821156818412 0.55142736014289 chr7 159138663 11462554 0.07202871875327996 1.0521781237115786 chr8 146364022 20112567 0.13741469197942646 0.822681368162742 chr9 141213431 9975525 0.07064147460591054 0.8580228989515734 chr10 135534747 12065746 0.08902326722165202 0.9912766486579034 chr11 135006516 8022433 0.0594225615006612 0.5757638396865256 chr12 133851895 9831899 0.07345356597304804 0.5424706857307927 chr13 115169878 4723779 0.04101575066355458 0.3906166676673144 chr14 107349540 5208102 0.04851536392237917 0.45857024221685666 chr15 102531392 6015944 0.05867416683468025 0.47701031876840955 chr16 90354753 7598389 0.08409506691916915 1.0001578053000526 chr17 81195210 7808667 0.09617152292604453 0.7038458643682691 chr18 78077248 5494693 0.07037508545383157 0.9705225210134918 chr19 59128983 4888371 0.08267300995182007 1.4070550832717692 chr20 63025520 6769488 0.10740868143571049 0.6905488720562515 chr21 48129895 3218892 0.06687926495580346 0.5533275974201829 chr22 51304566 1862593 0.03630462442660562 0.416421539807796 chrMT 16571 128604 7.760786916903023 7.041906641458738 chrX 155270560 13879243 0.0893874730663688 0.6845321976543773 chrY 59373566 840798 0.014161150435195353 0.8743756770064575