BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818993.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 = 2,260,033 number of mapped reads = 2,223,486 (98.38%) number of supplementary alignments = 33,949 (1.5%) number of secondary alignments = 0 number of mapped bases = 205,735,511 bp number of sequenced bases = 205,612,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 944,635 duplication rate = 35.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2562 >>>>>>> ACTG content number of A's = 61,137,813 bp (29.73%) number of C's = 43,385,637 bp (21.1%) number of T's = 57,038,294 bp (27.74%) number of G's = 44,040,500 bp (21.42%) number of N's = 9,917 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,282,281 number of insertions = 37,156 mapped reads with insertion percentage = 1.62% number of deletions = 67,302 mapped reads with deletion percentage = 2.96% homopolymer indels = 41.74% >>>>>>> Coverage mean coverageData = 0.0665X std coverageData = 0.7432X There is a 3.21% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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% 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 19951277 0.080045044301013 1.289225369089837 chr2 243199373 16458827 0.06767627233973172 1.0817889492736024 chr3 198022430 11770340 0.05943942814962931 0.43595696010460677 chr4 191154276 11769780 0.06157215128161716 0.5247937665120419 chr5 180915260 11780704 0.06511724881582681 0.46814386062089713 chr6 171115067 8453664 0.049403387721549966 0.4873346859938702 chr7 159138663 9844165 0.061859040502307096 0.834440790653729 chr8 146364022 18514676 0.1264974530421144 0.723625455363361 chr9 141213431 9177736 0.06499194825172118 0.7097072123594516 chr10 135534747 10727369 0.07914847843409484 0.9018836250585135 chr11 135006516 6645527 0.04922375005958972 0.49625074233301036 chr12 133851895 9856652 0.0736384942476907 0.4960527986011805 chr13 115169878 4822939 0.04187673968014449 0.3621761246047273 chr14 107349540 4743337 0.04418590894753718 0.4013707529889506 chr15 102531392 5169290 0.05041665678351465 0.40466672131746473 chr16 90354753 6884719 0.07619653390010374 0.8276463324879787 chr17 81195210 6883302 0.08477472993788673 0.6011443899877013 chr18 78077248 5018255 0.06427294927198254 0.8248862226356513 chr19 59128983 4124531 0.06975481042858457 1.1733753567334029 chr20 63025520 5612430 0.08905011811088588 0.5813675299490167 chr21 48129895 2825452 0.05870471980044835 0.48615256119406 chr22 51304566 1626281 0.03169856265814625 0.3540271572265694 chrMT 16571 28060 1.693319654818659 2.7532489878224546 chrX 155270560 12272161 0.07903726888084901 0.5748809538112587 chrY 59373566 774037 0.013036727489132116 0.8067678698212007