BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238327.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 = 1,853,262 number of mapped reads = 1,668,221 (90.02%) number of supplementary alignments = 15,077 (0.81%) number of secondary alignments = 0 number of mapped bases = 110,993,199 bp number of sequenced bases = 110,938,227 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,878 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2844 >>>>>>> ACTG content number of A's = 31,802,255 bp (28.67%) number of C's = 21,106,031 bp (19.03%) number of T's = 33,464,650 bp (30.17%) number of G's = 24,530,166 bp (22.11%) number of N's = 35,125 bp (0.03%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 993,036 number of insertions = 9,118 mapped reads with insertion percentage = 0.54% number of deletions = 31,738 mapped reads with deletion percentage = 1.88% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.4402X There is a 3.23% of reference with a coverageData >= 1X There is a 0.22% 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 10348974 0.0415203539252165 0.9181677827468981 chr2 243199373 8871205 0.03647708828591429 0.45337290322739315 chr3 198022430 7536874 0.03806070857730612 0.20958325518973453 chr4 191154276 6619283 0.03462796197140785 0.2231044143387318 chr5 180915260 7320862 0.04046569648132502 0.22081099102167995 chr6 171115067 6512415 0.03805868830942865 0.26751154369650393 chr7 159138663 5605479 0.03522386637117845 0.5381341874280509 chr8 146364022 5319973 0.03634754584702517 0.7482039215818511 chr9 141213431 4531144 0.03208720281004999 0.4093650655468642 chr10 135534747 5350798 0.03947916027762239 0.3817511202539676 chr11 135006516 4964692 0.03677372135134574 0.34760983951940966 chr12 133851895 5636050 0.04210661343270486 0.2288371645193911 chr13 115169878 2626758 0.02280768240459541 0.16012675787858202 chr14 107349540 3030461 0.028229846164222035 0.23489753662780488 chr15 102531392 3209021 0.03129793653830429 0.19402133555969425 chr16 90354753 2863291 0.031689434201651795 0.22756776335595535 chr17 81195210 2720289 0.03350307241030598 0.23061309545178743 chr18 78077248 3239061 0.041485337700427144 0.748249391112653 chr19 59128983 2128847 0.03600344352278138 0.5758080644827169 chr20 63025520 2425684 0.038487330211634904 0.22086996121515204 chr21 48129895 1312339 0.027266608414583077 0.2222322721051292 chr22 51304566 1115075 0.021734420285321195 0.15605109978933532 chrMT 16571 104961 6.3340172590670445 4.7076197951806575 chrX 155270560 7274020 0.04684738690966272 0.2704458781621492 chrY 59373566 325643 0.005484646147074946 0.1501779282897988