BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472442.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,481,310 number of mapped reads = 12,925,195 (95.87%) number of supplementary alignments = 51,203 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,272,455 number of mapped paired reads (second in pair) = 6,652,740 number of mapped paired reads (both in pair) = 12,431,704 number of mapped paired reads (singletons) = 493,491 number of mapped bases = 1,254,771,624 bp number of sequenced bases = 1,254,629,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,566,687 duplication rate = 44.18% >>>>>>> Insert size mean insert size = 21,460.0404 std insert size = 1,414,686.674 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.3418 >>>>>>> ACTG content number of A's = 346,420,611 bp (27.61%) number of C's = 289,217,960 bp (23.05%) number of T's = 333,037,965 bp (26.54%) number of G's = 285,795,581 bp (22.78%) number of N's = 157,838 bp (0.01%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 11,946,715 number of insertions = 77,843 mapped reads with insertion percentage = 0.6% number of deletions = 60,614 mapped reads with deletion percentage = 0.46% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.4053X std coverageData = 13.4673X There is a 3.86% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 119178912 0.47814890699911233 13.747001113911944 chr2 243199373 107356335 0.44143343659031553 15.012131762837981 chr3 198022430 72741080 0.3673375788793219 8.776165166163972 chr4 191154276 31359936 0.16405563430869838 6.429476054611236 chr5 180915260 53292049 0.2945691203716038 14.481368449011532 chr6 171115067 103442013 0.6045172690725125 15.94457585692897 chr7 159138663 88518218 0.5562332643199346 15.774589934744679 chr8 146364022 114007847 0.7789335483005516 23.729305849426485 chr9 141213431 42306297 0.2995911699079105 7.731649817790555 chr10 135534747 19754145 0.14574967259133925 5.0536328657767156 chr11 135006516 42040182 0.31139372561839906 11.153488204115098 chr12 133851895 68909566 0.5148195025554176 14.924033694345201 chr13 115169878 49489188 0.4297060035090078 17.113463882970336 chr14 107349540 36349376 0.33860765495595047 12.977732116145074 chr15 102531392 19925594 0.1943365208579242 6.790583090666073 chr16 90354753 45302237 0.5013818918856432 13.15730724065103 chr17 81195210 53432368 0.6580729084880746 14.573754351616708 chr18 78077248 10029652 0.12845806245629968 5.536573830459461 chr19 59128983 36038571 0.6094907974317773 14.859852898784847 chr20 63025520 55276490 0.8770493285894349 23.775108755101833 chr21 48129895 8063358 0.16753325557847154 7.923703779253792 chr22 51304566 11458816 0.22334885358936668 8.880803493379862 chrMT 16571 2104 0.1269688009172651 0.39860186850133056 chrX 155270560 66225755 0.42651842693167336 13.123089374608789 chrY 59373566 271535 0.004573331505808494 0.41827831350259215