BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525089.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 = 4,812,794 number of mapped reads = 4,332,487 (90.02%) number of supplementary alignments = 19,851 (0.41%) number of secondary alignments = 0 number of mapped bases = 249,328,877 bp number of sequenced bases = 249,265,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 277,476 duplication rate = 4.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5642 >>>>>>> ACTG content number of A's = 65,084,415 bp (26.11%) number of C's = 47,258,735 bp (18.96%) number of T's = 78,924,062 bp (31.66%) number of G's = 57,990,821 bp (23.26%) number of N's = 7,599 bp (0%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,172,619 number of insertions = 17,989 mapped reads with insertion percentage = 0.41% number of deletions = 38,191 mapped reads with deletion percentage = 0.88% homopolymer indels = 41.55% >>>>>>> Coverage mean coverageData = 0.0805X std coverageData = 0.5684X There is a 6.36% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 17558004 0.07044317053075667 1.0028121332287367 chr2 243199373 21098421 0.0867535994839921 0.6418569932026025 chr3 198022430 16856648 0.08512494266432342 0.3555598583224343 chr4 191154276 17149477 0.08971537210080512 0.42940170413628664 chr5 180915260 16050284 0.08871713751509962 0.3689067580277582 chr6 171115067 14719349 0.08602018079448258 0.4016062725593713 chr7 159138663 13710800 0.08615631011051035 0.7011168045855315 chr8 146364022 13225704 0.09036171471155664 0.7266989001722126 chr9 141213431 10576078 0.07489427829283463 0.5655651782711829 chr10 135534747 12265830 0.09049952334363379 0.5653746148499542 chr11 135006516 11128534 0.08242960658284079 0.5206656278365116 chr12 133851895 11284033 0.08430237763910627 0.37630945908804514 chr13 115169878 8048829 0.06988658093394871 0.31967409426140053 chr14 107349540 7517532 0.07002854413721754 0.3713606567429368 chr15 102531392 7142084 0.06965753473823899 0.3247906547893628 chr16 90354753 7333894 0.08116777210380953 0.38760277210238775 chr17 81195210 6298376 0.07757078280849326 0.37494241076360396 chr18 78077248 6475305 0.08293459574804686 1.017359519386109 chr19 59128983 4195373 0.07095290307969612 0.7738702088648993 chr20 63025520 5415109 0.08591930697279451 0.37975990321999964 chr21 48129895 3256461 0.0676598401056142 0.3913935598000221 chr22 51304566 2858847 0.05572305201841099 0.28688171355406006 chrMT 16571 116848 7.051354776416631 4.715515055404467 chrX 155270560 14366245 0.09252394658717017 0.45994742985716774 chrY 59373566 680812 0.01146658430453714 0.24557039640758732