BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472812.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 = 2,903,795 number of mapped reads = 2,340,411 (80.6%) number of supplementary alignments = 22,153 (0.76%) number of secondary alignments = 0 number of mapped bases = 148,409,895 bp number of sequenced bases = 148,346,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,977 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4111 >>>>>>> ACTG content number of A's = 39,949,943 bp (26.93%) number of C's = 29,547,271 bp (19.92%) number of T's = 43,951,921 bp (29.63%) number of G's = 34,894,438 bp (23.52%) number of N's = 3,404 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,308,731 number of insertions = 11,404 mapped reads with insertion percentage = 0.48% number of deletions = 34,999 mapped reads with deletion percentage = 1.48% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.3669X There is a 3.96% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.05% 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% 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 12413674 0.04980398423962201 0.46221288648524717 chr2 243199373 12977296 0.05336072967589436 0.5130251331650227 chr3 198022430 11204938 0.056584185942976255 0.28261613000402463 chr4 191154276 6976706 0.03649777627783749 0.2577326664322028 chr5 180915260 8891805 0.04914900489875757 0.26656595202037675 chr6 171115067 10358690 0.06053639917050671 0.3205965197765176 chr7 159138663 8325262 0.05231451517221808 0.48162888109852586 chr8 146364022 7677882 0.05245744066803521 0.34359839178788865 chr9 141213431 6457728 0.045730267682540765 0.39320667492393024 chr10 135534747 5670029 0.041834504623378975 0.33961614284734093 chr11 135006516 5798730 0.042951482430670235 0.39986635580030605 chr12 133851895 7148995 0.05340974066896849 0.2848792278399967 chr13 115169878 6649505 0.0577364942593757 0.2919270190884279 chr14 107349540 3764943 0.035071813069716 0.2790323970002003 chr15 102531392 3545399 0.0345786683555413 0.24653702036202194 chr16 90354753 4461081 0.04937295329665723 0.2962906194360368 chr17 81195210 3799380 0.04679315442376465 0.284994267500188 chr18 78077248 3203547 0.04103048048004971 0.7085446026023027 chr19 59128983 3253464 0.055023168587222275 0.374413281324282 chr20 63025520 4822407 0.0765151481495115 0.35039209058164594 chr21 48129895 2064128 0.04288660924774509 0.2854391072546506 chr22 51304566 1620249 0.03158099027677186 0.2209836926111716 chrMT 16571 90645 5.470098364612878 4.309510979333917 chrX 155270560 6491141 0.04180535576093755 0.28763759661425575 chrY 59373566 742271 0.012501708251783294 0.1738546889817316