BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818830.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 = 1,929,026 number of mapped reads = 1,887,805 (97.86%) number of supplementary alignments = 39,839 (2.07%) number of secondary alignments = 0 number of mapped bases = 174,994,117 bp number of sequenced bases = 174,898,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 335,398 duplication rate = 14.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.6348 >>>>>>> ACTG content number of A's = 50,645,801 bp (28.96%) number of C's = 36,939,747 bp (21.12%) number of T's = 49,990,799 bp (28.58%) number of G's = 37,319,935 bp (21.34%) number of N's = 2,706 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,013,916 number of insertions = 22,859 mapped reads with insertion percentage = 1.18% number of deletions = 48,536 mapped reads with deletion percentage = 2.52% homopolymer indels = 41.4% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.5575X There is a 4.14% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 12542489 0.05032079338329913 0.6739890169247913 chr2 243199373 12950375 0.053250034489192535 0.6632334737062734 chr3 198022430 11416028 0.05765017629568529 0.3067744201819105 chr4 191154276 10505683 0.05495918385838253 0.4431792391352664 chr5 180915260 7756102 0.04287146368968544 0.2671149154528478 chr6 171115067 8624145 0.05039968222085318 0.3135664490043372 chr7 159138663 15477708 0.0972592562248685 1.306947550111478 chr8 146364022 17959371 0.12270345372170764 0.589446998879925 chr9 141213431 6301183 0.04462169749278311 0.519678405130419 chr10 135534747 8041455 0.05933131671393462 0.76093440999427 chr11 135006516 7629679 0.05651341302667199 0.3853884263529824 chr12 133851895 6878469 0.05138865609635187 0.2910535183018573 chr13 115169878 5646913 0.04903116247114545 0.2819876781285599 chr14 107349540 5339580 0.04974012930097325 0.30110706986952546 chr15 102531392 4834129 0.04714779450180487 0.27571157458698364 chr16 90354753 4328861 0.047909610244853414 0.4365687114045917 chr17 81195210 4396361 0.054145570902519986 0.447227632076065 chr18 78077248 3295979 0.042214333681433035 0.5567609117994099 chr19 59128983 2852739 0.04824603528188537 0.6073857839021852 chr20 63025520 7207267 0.11435474074628817 0.46890318186000085 chr21 48129895 1702829 0.03537986110295898 0.3438305758400839 chr22 51304566 1562627 0.03045785437498877 0.23589795449331274 chrMT 16571 142397 8.59314465029268 5.990029243193431 chrX 155270560 6909287 0.04449837110138587 0.32154107529289455 chrY 59373566 692461 0.011662782727249361 0.7954952730820314