BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777300.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,515,744 number of mapped reads = 1,486,089 (98.04%) number of supplementary alignments = 59,373 (3.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 744,577 number of mapped paired reads (second in pair) = 741,512 number of mapped paired reads (both in pair) = 1,478,406 number of mapped paired reads (singletons) = 7,683 number of mapped bases = 143,388,182 bp number of sequenced bases = 143,325,372 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,644 duplication rate = 7.66% >>>>>>> Insert size mean insert size = 162,320.1566 std insert size = 3,847,368.3163 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.8287 >>>>>>> ACTG content number of A's = 42,701,918 bp (29.79%) number of C's = 29,116,038 bp (20.31%) number of T's = 41,910,589 bp (29.24%) number of G's = 29,594,591 bp (20.65%) number of N's = 2,236 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 888,724 number of insertions = 36,088 mapped reads with insertion percentage = 2.34% number of deletions = 22,350 mapped reads with deletion percentage = 1.44% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 0.6903X There is a 3.22% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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% 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 11473647 0.04603257136920032 1.1492961643385022 chr2 243199373 12793233 0.052603889731245315 0.6344038128423416 chr3 198022430 9826197 0.04962163629645389 0.3513547359586741 chr4 191154276 10025428 0.052446789105570414 0.6383627361675793 chr5 180915260 8805333 0.04867103526811392 0.284096638435649 chr6 171115067 8378293 0.04896291803456443 0.3434301425348416 chr7 159138663 7563604 0.04752838724050359 0.4731830119941779 chr8 146364022 7340233 0.05015052811270792 0.43385053850843813 chr9 141213431 6013997 0.04258799575516298 0.5636179992295511 chr10 135534747 8143930 0.06008739589118058 1.9552427256148337 chr11 135006516 6469033 0.04791645019563352 0.3293037766039574 chr12 133851895 6445875 0.04815677058587777 0.29026062610984377 chr13 115169878 4762482 0.04135180207449729 0.2632580050332636 chr14 107349540 4279154 0.03986187551432451 0.26604952981636343 chr15 102531392 3790321 0.03696741969522856 0.24386805777006282 chr16 90354753 4943776 0.05471517364448996 0.9223101738368082 chr17 81195210 3316634 0.040847655914677726 0.3791459040733848 chr18 78077248 4052849 0.051908194817522256 0.7291637634894822 chr19 59128983 2165842 0.036629109619558314 0.6548696411524668 chr20 63025520 2729971 0.043315326870766 0.29523877821840494 chr21 48129895 1954828 0.040615671403396995 0.3463663442323806 chr22 51304566 1282092 0.024989822543280065 0.21676196042893964 chrMT 16571 555998 33.552471184599604 11.437303171807786 chrX 155270560 4186725 0.026964061957398748 0.23246309196875567 chrY 59373566 2088707 0.03517907278804847 0.8080958402810066