BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524327.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,123,364 number of mapped reads = 2,856,783 (91.46%) number of supplementary alignments = 12,963 (0.42%) number of secondary alignments = 0 number of mapped bases = 165,827,329 bp number of sequenced bases = 165,782,043 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,796 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7998 >>>>>>> ACTG content number of A's = 41,668,072 bp (25.13%) number of C's = 29,995,411 bp (18.09%) number of T's = 51,683,355 bp (31.18%) number of G's = 42,411,284 bp (25.58%) number of N's = 23,921 bp (0.01%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 844,340 number of insertions = 11,060 mapped reads with insertion percentage = 0.39% number of deletions = 28,639 mapped reads with deletion percentage = 1% homopolymer indels = 41.79% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.4557X There is a 4.6% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13962404 0.05601752944077921 0.8948128430347813 chr2 243199373 10788870 0.04436224430562163 0.6136637394170587 chr3 198022430 11747287 0.05932301204464565 0.2789304519746532 chr4 191154276 8696137 0.04549276731847735 0.28497367483322117 chr5 180915260 9786116 0.05409226396933017 0.2643480550278571 chr6 171115067 10400369 0.060779972110813596 0.31247677796254375 chr7 159138663 7524196 0.04728075414332217 0.5960352488757104 chr8 146364022 16477785 0.11258084312550526 0.5396150346107345 chr9 141213431 6993937 0.04952742066014953 0.35390653897758323 chr10 135534747 8543895 0.06303841036424408 0.45263109904755217 chr11 135006516 7856496 0.05819345786243384 0.3659554980587553 chr12 133851895 6654185 0.04971304291209325 0.26045625195513916 chr13 115169878 4345578 0.03773189722402936 0.218848506145907 chr14 107349540 3492010 0.032529342929648326 0.22764474570593748 chr15 102531392 5019051 0.048951359209089836 0.2601091631620021 chr16 90354753 5790534 0.06408665629355437 0.3134147048578643 chr17 81195210 4898349 0.06032805383470281 0.31968593458043587 chr18 78077248 3920134 0.050208403861775455 0.6686307166459936 chr19 59128983 2954969 0.04997496743686594 0.5872681600430867 chr20 63025520 3858044 0.06121399712370481 0.2921602656715268 chr21 48129895 2435318 0.05059886376232485 0.28780634732702276 chr22 51304566 1234395 0.024060139208662245 0.17755371157494573 chrMT 16571 9456 0.5706354474684691 0.8621781184207478 chrX 155270560 7968516 0.05132019875499902 0.3050555548250096 chrY 59373566 469298 0.007904157213666432 0.216612367033569