BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975312.sorted.bam outfile = /mainsd/zhouyj/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 = 2,399,276 number of mapped reads = 2,331,338 (97.17%) number of supplementary alignments = 24,325 (1.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,187,764 number of mapped paired reads (second in pair) = 1,143,574 number of mapped paired reads (both in pair) = 2,283,760 number of mapped paired reads (singletons) = 47,578 number of mapped bases = 312,817,378 bp number of sequenced bases = 312,603,110 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 333,351 duplication rate = 14.09% >>>>>>> Insert size mean insert size = 71,303.2561 std insert size = 2,555,826.6427 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 53.6544 >>>>>>> ACTG content number of A's = 90,559,807 bp (28.97%) number of C's = 63,983,172 bp (20.47%) number of T's = 90,499,674 bp (28.95%) number of G's = 67,542,008 bp (21.61%) number of N's = 18,449 bp (0.01%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 3,991,411 number of insertions = 56,666 mapped reads with insertion percentage = 2.32% number of deletions = 114,734 mapped reads with deletion percentage = 4.75% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.101X std coverageData = 1.0656X There is a 5.82% of reference with a coverageData >= 1X There is a 3.15% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 27607711 0.11076285743737425 1.1376139129378031 chr2 243199373 27075707 0.11133131909842547 1.1531005406799122 chr3 198022430 21307593 0.1076019166111637 0.45822763063139577 chr4 191154276 18907981 0.09891476871801706 0.7212307445432685 chr5 180915260 18983836 0.10493219864371861 0.4489533881543724 chr6 171115067 21740065 0.1270493906886645 1.2832405028670748 chr7 159138663 16515776 0.10378229707761212 1.1430842723456118 chr8 146364022 17094661 0.1167955127661086 0.5591431481532788 chr9 141213431 13754835 0.09740458044674236 1.8356198535781245 chr10 135534747 15780656 0.11643254847408244 2.313652313986348 chr11 135006516 14055375 0.10410886390105793 1.0855742308730947 chr12 133851895 13811623 0.10318586076050698 0.44331464940019066 chr13 115169878 8096440 0.0702999789580397 0.36168039456170215 chr14 107349540 9397063 0.08753705884533833 0.4232108354966211 chr15 102531392 9605681 0.09368526860534576 0.42672016342478625 chr16 90354753 10773858 0.11923952689019027 1.4813569449540405 chr17 81195210 7717245 0.09504556980639621 1.1889786200282226 chr18 78077248 8821624 0.11298584704214984 1.644681204964413 chr19 59128983 4561477 0.07714451980342703 0.7134173720510671 chr20 63025520 7019632 0.11137761338581578 0.505263584181945 chr21 48129895 4068515 0.08453197331928523 0.5363116124565033 chr22 51304566 3464303 0.06752426285021103 0.361126983693274 chrMT 16571 94359 5.694224850642689 4.146349515271974 chrX 155270560 9160971 0.05900005126535256 0.4624854446365175 chrY 59373566 3400391 0.05727112634602409 1.235561018545251