BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975203.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/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 = 2,960,846 number of mapped reads = 2,926,411 (98.84%) number of supplementary alignments = 39,889 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,464,862 number of mapped paired reads (second in pair) = 1,461,549 number of mapped paired reads (both in pair) = 2,916,584 number of mapped paired reads (singletons) = 9,827 number of mapped bases = 401,915,815 bp number of sequenced bases = 401,603,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 503,165 duplication rate = 14.69% >>>>>>> Insert size mean insert size = 83,537.6558 std insert size = 2,772,142.9328 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 53.3834 >>>>>>> ACTG content number of A's = 119,805,229 bp (29.83%) number of C's = 79,517,610 bp (19.8%) number of T's = 119,550,381 bp (29.77%) number of G's = 82,705,640 bp (20.59%) number of N's = 24,754 bp (0.01%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 4,557,045 number of insertions = 88,490 mapped reads with insertion percentage = 2.85% number of deletions = 149,040 mapped reads with deletion percentage = 4.88% homopolymer indels = 44.78% >>>>>>> Coverage mean coverageData = 0.1298X std coverageData = 2.2972X There is a 6.75% of reference with a coverageData >= 1X There is a 3.84% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 35590561 0.1427902600892617 2.2320742239085147 chr2 243199373 28165421 0.11581206255823694 1.9899344171732227 chr3 198022430 35452877 0.17903465279160546 0.7484267936154367 chr4 191154276 22357625 0.11696115550143382 1.4267872181230554 chr5 180915260 31737954 0.17542994438390658 0.6380973607395646 chr6 171115067 20661596 0.12074679548820795 0.8932832716084971 chr7 159138663 16763992 0.10534204374960722 1.1100493890018164 chr8 146364022 24360070 0.1664348223499898 0.9151042403680422 chr9 141213431 13926955 0.09862344467786495 2.7046122219522486 chr10 135534747 22276259 0.1643582881369897 8.319481686929947 chr11 135006516 15545316 0.11514493122687501 0.9877270999098724 chr12 133851895 14720598 0.10997676200251032 0.4925390787511463 chr13 115169878 9294645 0.08070378436972904 0.41134856559347743 chr14 107349540 11418587 0.10636828998056257 0.5115517676822878 chr15 102531392 8679109 0.08464830946604139 0.42381453263547164 chr16 90354753 12895310 0.14271866804837594 3.2362170553095746 chr17 81195210 7050313 0.0868316369894234 1.6209290739863917 chr18 78077248 12795229 0.163879098300186 2.667903583593302 chr19 59128983 5481713 0.09270771662012181 1.1224048995855038 chr20 63025520 7545796 0.11972604113381373 0.7099064766975862 chr21 48129895 4359301 0.0905736652864088 0.8690285974333405 chr22 51304566 2841122 0.055377566199468486 0.35812791734541954 chrMT 16571 148742 8.976042483857341 6.580520428634163 chrX 155270560 34523119 0.22234169181846192 0.9410196679439066 chrY 59373566 3323605 0.05597785721679577 2.7524903310672415