BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926931.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 12,063,998 number of mapped reads = 11,783,296 (97.67%) number of supplementary alignments = 78,415 (0.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,908,348 number of mapped paired reads (second in pair) = 5,874,948 number of mapped paired reads (both in pair) = 11,690,880 number of mapped paired reads (singletons) = 92,416 number of mapped bases = 1,114,307,990 bp number of sequenced bases = 1,113,442,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 530,114 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 68,488.4276 std insert size = 2,547,968.6756 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.6134 >>>>>>> ACTG content number of A's = 320,166,783 bp (28.75%) number of C's = 221,488,372 bp (19.89%) number of T's = 323,616,413 bp (29.06%) number of G's = 247,927,426 bp (22.27%) number of N's = 243,792 bp (0.02%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 10,433,125 number of insertions = 181,862 mapped reads with insertion percentage = 1.52% number of deletions = 611,698 mapped reads with deletion percentage = 5.05% homopolymer indels = 53.08% >>>>>>> Coverage mean coverageData = 0.36X std coverageData = 1.7152X There is a 20.07% of reference with a coverageData >= 1X There is a 8.34% of reference with a coverageData >= 2X There is a 3.55% of reference with a coverageData >= 3X There is a 1.66% of reference with a coverageData >= 4X There is a 0.81% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 93758253 0.3761605592950559 2.51378583594188 chr2 243199373 99711462 0.40999884485721927 2.6428874458860063 chr3 198022430 72850825 0.3678917837741916 0.913752221460815 chr4 191154276 72564753 0.37961354837806505 1.6157791279618705 chr5 180915260 69769769 0.3856488888775883 0.933163037319691 chr6 171115067 65073947 0.38029349572121546 1.5024070545834494 chr7 159138663 52766919 0.3315782475814818 1.0215678334395915 chr8 146364022 57559309 0.3932613234692334 1.1088512693901578 chr9 141213431 47275207 0.3347784036208284 1.9613597178868003 chr10 135534747 55382194 0.4086198943507822 3.610998998347746 chr11 135006516 52029084 0.38538202111666964 1.3697413769163793 chr12 133851895 49224310 0.3677520590948675 0.9404743932386818 chr13 115169878 32576271 0.2828540896778583 0.7904400445010231 chr14 107349540 31128341 0.28997181543581835 0.8341666481636716 chr15 102531392 30511302 0.2975801011264921 0.8338755238995469 chr16 90354753 32078293 0.3550260715117001 1.7468448909743106 chr17 81195210 28428433 0.3501245085763064 1.141713204516818 chr18 78077248 32090150 0.4110051368613812 2.14591576486577 chr19 59128983 17456610 0.2952293294136312 1.4964626063404498 chr20 63025520 25924502 0.4113334090698498 1.071062442522988 chr21 48129895 14364266 0.29844789813067324 1.192524196084669 chr22 51304566 12631564 0.24620740384004028 0.7981368630875393 chrMT 16571 796993 48.09564902540583 35.690297020158816 chrX 155270560 66506486 0.42832643870158 1.0993410987064902 chrY 59373566 1848747 0.031137543599789846 1.1103911704148641