BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716736.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,719,933 number of mapped reads = 1,550,464 (90.15%) number of supplementary alignments = 8,237 (0.48%) number of secondary alignments = 0 number of mapped bases = 89,577,369 bp number of sequenced bases = 89,552,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,245 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.046 >>>>>>> ACTG content number of A's = 21,815,153 bp (24.36%) number of C's = 17,880,009 bp (19.97%) number of T's = 28,904,141 bp (32.28%) number of G's = 20,952,391 bp (23.4%) number of N's = 1,101 bp (0%) GC percentage = 43.36% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 441,986 number of insertions = 6,680 mapped reads with insertion percentage = 0.43% number of deletions = 15,761 mapped reads with deletion percentage = 1.01% homopolymer indels = 40.43% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2732X There is a 2.63% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 7678979 0.030808264265066766 0.437610197327098 chr2 243199373 9248247 0.03802742945394025 0.326890445624797 chr3 198022430 6420219 0.032421675665731405 0.2004214612045299 chr4 191154276 5226463 0.027341596062439116 0.1875080169795996 chr5 180915260 5069152 0.028019482712514136 0.18026654095840533 chr6 171115067 5254419 0.03070693359807994 0.20378025418679074 chr7 159138663 4537653 0.028513831362275553 0.5220211279147036 chr8 146364022 6504776 0.04444245184790016 0.28763712074004455 chr9 141213431 3753989 0.026583795701415964 0.2050793709731042 chr10 135534747 4436173 0.032730890772976466 0.3345861802374169 chr11 135006516 2686718 0.0199006542765684 0.18812304321205803 chr12 133851895 4275651 0.0319431488063729 0.20556885135780695 chr13 115169878 2397206 0.020814522352797838 0.15415156924056359 chr14 107349540 2287966 0.02131323525000666 0.16487034374713183 chr15 102531392 1936235 0.018884313986491083 0.15626814252496352 chr16 90354753 2757815 0.030522080006128733 0.19787339350505367 chr17 81195210 3581666 0.04411178935309115 0.23404217625557983 chr18 78077248 2005914 0.025691402442872987 0.310326337383129 chr19 59128983 1685345 0.0285028578962706 0.36472407093866865 chr20 63025520 2037143 0.032322509992777526 0.1984564786998998 chr21 48129895 946309 0.019661563774448294 0.1548426725249214 chr22 51304566 1315537 0.02564171383888132 0.17303252433089253 chrMT 16571 42376 2.5572385492728262 2.033196945446657 chrX 155270560 3306588 0.021295653213332908 0.18273788468738286 chrY 59373566 184830 0.003113001499690957 0.0816093452344475