BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975197.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,227,774 number of mapped reads = 2,202,912 (98.88%) number of supplementary alignments = 29,152 (1.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,102,842 number of mapped paired reads (second in pair) = 1,100,070 number of mapped paired reads (both in pair) = 2,195,440 number of mapped paired reads (singletons) = 7,472 number of mapped bases = 301,991,446 bp number of sequenced bases = 301,756,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 379,120 duplication rate = 15.96% >>>>>>> Insert size mean insert size = 95,332.505 std insert size = 2,974,425.5011 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 53.4787 >>>>>>> ACTG content number of A's = 89,690,805 bp (29.72%) number of C's = 60,314,513 bp (19.99%) number of T's = 89,151,354 bp (29.54%) number of G's = 62,583,298 bp (20.74%) number of N's = 16,202 bp (0.01%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 3,736,645 number of insertions = 67,176 mapped reads with insertion percentage = 2.89% number of deletions = 127,097 mapped reads with deletion percentage = 5.54% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.0976X std coverageData = 1.5503X There is a 5.29% of reference with a coverageData >= 1X There is a 2.98% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 24944857 0.10007941765569363 1.7556144461700653 chr2 243199373 21921765 0.0901390687384708 1.2383762712508615 chr3 198022430 26151042 0.13206100945231306 0.5875007991523389 chr4 191154276 17208280 0.09002299273702881 0.7653572481936233 chr5 180915260 28194565 0.15584403991128223 0.5876631522295191 chr6 171115067 15662534 0.09153217349352409 0.6726181687299156 chr7 159138663 13769846 0.08652734502362885 0.8332256023514596 chr8 146364022 15725452 0.10744069331464531 0.5947413535260636 chr9 141213431 10988329 0.07781362524928666 1.6926514855563484 chr10 135534747 16403063 0.12102478045722105 5.458442235240373 chr11 135006516 12215333 0.09047958100037186 0.7750298493599656 chr12 133851895 11255544 0.08408953791801005 0.41648693411620075 chr13 115169878 6531356 0.056710627061704454 0.33818835787223805 chr14 107349540 9217090 0.08586054490778441 0.43557018055347474 chr15 102531392 6938950 0.06767634638179885 0.3720377981268533 chr16 90354753 10132265 0.11213870508837537 2.570146656405986 chr17 81195210 5201934 0.06406700592313266 1.1900690942734442 chr18 78077248 7620927 0.09760752581853295 1.7123915077661145 chr19 59128983 4681754 0.07917866606973437 1.0082714646745308 chr20 63025520 4991696 0.07920118707469609 0.46853078791420294 chr21 48129895 3710511 0.07709368574354879 0.5591370606075378 chr22 51304566 2510680 0.048936774945138414 0.3265123214145389 chrMT 16571 51296 3.095528332629292 2.6529704832613885 chrX 155270560 24827426 0.1598978325318077 0.7374339010773515 chrY 59373566 1134951 0.01911542587824353 1.289608396821051