BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094055.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 453,752 number of mapped reads = 431,281 (95.05%) number of supplementary alignments = 18,961 (4.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 216,587 number of mapped paired reads (second in pair) = 214,694 number of mapped paired reads (both in pair) = 428,518 number of mapped paired reads (singletons) = 2,763 number of mapped bases = 57,579,303 bp number of sequenced bases = 56,177,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 412,127 duplication rate = 50.23% >>>>>>> Insert size mean insert size = 537,202.6298 std insert size = 6,620,356.295 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 44.8877 >>>>>>> ACTG content number of A's = 15,598,048 bp (27.77%) number of C's = 12,554,095 bp (22.35%) number of T's = 14,947,811 bp (26.61%) number of G's = 13,077,093 bp (23.28%) number of N's = 674 bp (0%) GC percentage = 45.63% >>>>>>> Mismatches and indels general error rate = 0.0431 number of mismatches = 2,348,202 number of insertions = 40,356 mapped reads with insertion percentage = 9.19% number of deletions = 186,231 mapped reads with deletion percentage = 40.18% homopolymer indels = 28.6% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 4.8833X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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% 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 1161478 0.004659880065053077 2.0186584332735724 chr2 243199373 2595182 0.01067100612960873 3.566172341847636 chr3 198022430 1952405 0.009859514399454648 3.0953851189354316 chr4 191154276 1827003 0.00955774068062176 3.0692155688202725 chr5 180915260 358418 0.001981137467342445 0.5756782481439593 chr6 171115067 1955335 0.011427018288225899 4.9076874738446925 chr7 159138663 1141522 0.007173128003469528 1.8499568917887599 chr8 146364022 1107759 0.007568519810148426 2.0803084334284123 chr9 141213431 950819 0.006733205143921473 2.756652686691365 chr10 135534747 1045742 0.007715674564250302 2.962533421725498 chr11 135006516 1298368 0.00961707655651228 2.5958234747049618 chr12 133851895 2438531 0.018218128327581764 4.971530674011772 chr13 115169878 1402438 0.012177124994436479 3.6387788998654527 chr14 107349540 360225 0.0033556268615589782 1.3510341277627642 chr15 102531392 605684 0.005907303004332566 1.6119622367369353 chr16 90354753 538269 0.005957284837024567 1.7757600641544617 chr17 81195210 1216724 0.014985169691660383 3.6457025252552624 chr18 78077248 288201 0.003691228973644153 1.0913882296723851 chr19 59128983 262380 0.004437417771924134 0.8920024468238584 chr20 63025520 439254 0.006969462528829591 2.0651143453483614 chr21 48129895 106516 0.0022130943772056847 0.5719716958545944 chr22 51304566 175880 0.003428154913151395 0.8031474048492183 chrMT 16571 4474482 270.01882807313984 1090.8321762323305 chrX 155270560 29540278 0.19025034752241507 13.739358268576169 chrY 59373566 336410 0.005665989474171048 1.4571693308728328