BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236068.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 = 495,772 number of mapped reads = 426,320 (85.99%) number of supplementary alignments = 3,230 (0.65%) number of secondary alignments = 0 number of mapped bases = 28,102,883 bp number of sequenced bases = 28,089,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,889 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8269 >>>>>>> ACTG content number of A's = 7,751,059 bp (27.59%) number of C's = 5,020,703 bp (17.87%) number of T's = 9,063,960 bp (32.27%) number of G's = 6,239,397 bp (22.21%) number of N's = 14,262 bp (0.05%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 233,004 number of insertions = 2,007 mapped reads with insertion percentage = 0.47% number of deletions = 7,607 mapped reads with deletion percentage = 1.76% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0091X std coverageData = 0.1264X There is a 0.84% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2932516 0.011765330767220035 0.1938741607296644 chr2 243199373 2249756 0.00925066529673989 0.14056571172648755 chr3 198022430 1527386 0.0077131969343068865 0.09284009709706524 chr4 191154276 1616431 0.008456159254318748 0.09791258457618346 chr5 180915260 1072371 0.0059274767645360596 0.08199163767909802 chr6 171115067 2314682 0.013527049608086235 0.1461433128353634 chr7 159138663 1648670 0.010359958849220694 0.14793544641313078 chr8 146364022 2079977 0.01421098553850891 0.19041350508371788 chr9 141213431 1170695 0.008290252504381116 0.11555427678115757 chr10 135534747 1408896 0.010395090788047142 0.11952231515319368 chr11 135006516 1132213 0.008386358181408074 0.11556110443325078 chr12 133851895 848640 0.006340141841099821 0.08437280136481608 chr13 115169878 583196 0.005063789335610827 0.07523720337861639 chr14 107349540 1141594 0.010634363221304908 0.11014805113529672 chr15 102531392 493640 0.004814525486984513 0.07355754268896172 chr16 90354753 1000247 0.011070220069109148 0.11279651582398985 chr17 81195210 592828 0.007301268141310306 0.09567711033726199 chr18 78077248 1197300 0.01533481303029533 0.18516261480952592 chr19 59128983 506025 0.008557985852724713 0.15372603322023679 chr20 63025520 682482 0.010828661151863563 0.11015052514842666 chr21 48129895 582939 0.012111786240132042 0.11763131122402484 chr22 51304566 231253 0.004507454560672046 0.07035056192787877 chrMT 16571 12062 0.7278981352966025 0.9044462710411153 chrX 155270560 1008757 0.006496769252329611 0.08854574099403753 chrY 59373566 68327 0.0011507983199122653 0.039948350569310426