BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819089.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,825,579 number of mapped reads = 1,678,969 (91.97%) number of supplementary alignments = 7,157 (0.39%) number of secondary alignments = 0 number of mapped bases = 98,024,867 bp number of sequenced bases = 97,993,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,852 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8439 >>>>>>> ACTG content number of A's = 23,344,678 bp (23.82%) number of C's = 20,118,588 bp (20.53%) number of T's = 31,246,835 bp (31.89%) number of G's = 23,282,310 bp (23.76%) number of N's = 1,384 bp (0%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 494,072 number of insertions = 6,845 mapped reads with insertion percentage = 0.41% number of deletions = 18,847 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.2886X There is a 2.82% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% 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% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 9673592 0.03881070370532798 0.5405041714842598 chr2 243199373 7669718 0.03153675071358017 0.3300152975569899 chr3 198022430 5391956 0.027229016430108447 0.18400297928294312 chr4 191154276 5448299 0.02850210371438408 0.20945854971903063 chr5 180915260 5341270 0.029523601270561698 0.18883251108486745 chr6 171115067 4201829 0.024555575810282095 0.2208532038006324 chr7 159138663 4873623 0.030625009084058977 0.3640499814734931 chr8 146364022 8877302 0.06065221410764457 0.31461312145745357 chr9 141213431 4189059 0.029664734935871646 0.24176283437408033 chr10 135534747 5165177 0.038109614798631675 0.29317696312749136 chr11 135006516 3368126 0.024947877330602324 0.2646700713904572 chr12 133851895 4563154 0.03409106759377594 0.20384598384062308 chr13 115169878 2172080 0.018859792488449108 0.1515446649076951 chr14 107349540 2336300 0.021763484035422973 0.16861644289771274 chr15 102531392 2602848 0.025385864262917644 0.17951339026848076 chr16 90354753 3095849 0.034263266703855634 0.21772795899064593 chr17 81195210 3487720 0.04295475065585765 0.24179762421962628 chr18 78077248 2325903 0.02978976666800551 0.43860194973193367 chr19 59128983 2037181 0.03445317163665744 0.3704780192253066 chr20 63025520 2801512 0.0444504384890438 0.23427971085606433 chr21 48129895 1353681 0.028125575590804842 0.2015383502989047 chr22 51304566 823046 0.016042353813108954 0.13810286414473905 chrMT 16571 6617 0.39931205117373725 0.6997828123020893 chrX 155270560 5904646 0.03802811041578004 0.23979156987697467 chrY 59373566 314379 0.005294932091496745 0.14933257306883949