BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230363.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,219,788 number of mapped reads = 2,930,256 (91.01%) number of supplementary alignments = 24,329 (0.76%) number of secondary alignments = 0 number of mapped bases = 198,937,798 bp number of sequenced bases = 198,846,001 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,194 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2155 >>>>>>> ACTG content number of A's = 57,089,476 bp (28.71%) number of C's = 37,856,997 bp (19.04%) number of T's = 61,260,558 bp (30.81%) number of G's = 42,532,679 bp (21.39%) number of N's = 106,291 bp (0.05%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,802,263 number of insertions = 17,867 mapped reads with insertion percentage = 0.6% number of deletions = 53,405 mapped reads with deletion percentage = 1.8% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0643X std coverageData = 0.6586X There is a 4.94% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% 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 17070268 0.06848636096276767 1.4464235344829168 chr2 243199373 14538669 0.059780865471228004 0.7032664980360037 chr3 198022430 17402348 0.08788069109140818 0.37340982040617127 chr4 191154276 12281290 0.06424805270900663 0.39625711846242223 chr5 180915260 14782989 0.08171222814482317 0.3534287209128645 chr6 171115067 5953848 0.034794411178297936 0.255697315958221 chr7 159138663 6710331 0.04216656639876382 0.6643945436495706 chr8 146364022 12778044 0.08730317618628983 0.8428742162861154 chr9 141213431 9897956 0.0700921713317765 0.6158336964557428 chr10 135534747 12337207 0.09102615582408546 0.7316085384948043 chr11 135006516 5875357 0.04351906244288239 0.37239309157274647 chr12 133851895 4741353 0.03542238232787066 0.24855722007196818 chr13 115169878 9404301 0.08165590832700197 0.3502752212033152 chr14 107349540 6609158 0.061566710020368974 0.345107199954016 chr15 102531392 4418852 0.04309755201606938 0.2515928526803943 chr16 90354753 7026762 0.07776859287081445 0.48301242321698723 chr17 81195210 4238609 0.05220269767145131 0.32142540838794026 chr18 78077248 6943047 0.08892535505349779 1.2314542061630223 chr19 59128983 3958214 0.06694202739796827 0.9287766564872248 chr20 63025520 5071328 0.08046467526170352 0.3796595029181408 chr21 48129895 3083794 0.06407231929344537 0.382007971186654 chr22 51304566 2509849 0.04892057755639138 0.2698531540988971 chrMT 16571 3706 0.2236437149236618 0.5261756246227453 chrX 155270560 10665560 0.06869016251374375 0.38631068796624796 chrY 59373566 634958 0.010694287757619275 0.31168107593407063