BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716530.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 = 2,444,549 number of mapped reads = 2,314,076 (94.66%) number of supplementary alignments = 45,693 (1.87%) number of secondary alignments = 0 number of mapped bases = 184,581,889 bp number of sequenced bases = 184,499,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,423 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7828 >>>>>>> ACTG content number of A's = 46,120,879 bp (25%) number of C's = 36,443,499 bp (19.75%) number of T's = 56,443,826 bp (30.59%) number of G's = 45,478,235 bp (24.65%) number of N's = 12,561 bp (0.01%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,156,623 number of insertions = 14,215 mapped reads with insertion percentage = 0.6% number of deletions = 43,125 mapped reads with deletion percentage = 1.83% homopolymer indels = 42.96% >>>>>>> Coverage mean coverageData = 0.0596X std coverageData = 0.4705X There is a 4.92% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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% 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 15108454 0.06061551196696918 0.8039618537494726 chr2 243199373 15713664 0.06461227184167123 0.5947383857385216 chr3 198022430 12037700 0.06078957823111251 0.28519717852106474 chr4 191154276 11826394 0.06186832043453739 0.37871065154288563 chr5 180915260 11193333 0.06187058515682978 0.2935431762343568 chr6 171115067 10592632 0.06190356106981509 0.3226434896863886 chr7 159138663 9249556 0.05812261976839657 0.6362600679661 chr8 146364022 9446574 0.0645416398846979 0.5817261529721066 chr9 141213431 7866542 0.05570675497573598 0.44391712089655866 chr10 135534747 8924391 0.06584577901635807 0.49735607789934183 chr11 135006516 8442056 0.0625307299982469 0.4562028154811607 chr12 133851895 8352410 0.06240038663628931 0.2936545295936239 chr13 115169878 5783239 0.05021485739526441 0.26012473154989 chr14 107349540 5612763 0.052284928281946995 0.29034155331409617 chr15 102531392 5400725 0.05267386792134842 0.2668330179986584 chr16 90354753 5400909 0.059774486904966694 0.3166090250042282 chr17 81195210 5167249 0.0636398255512856 0.35350473927294035 chr18 78077248 5068021 0.06491034366375208 0.734396666606712 chr19 59128983 3796985 0.06421529353887247 0.587744455808683 chr20 63025520 4024966 0.06386247983356583 0.313749647907675 chr21 48129895 2487087 0.05167447383793378 0.322669530834257 chr22 51304566 2233385 0.04353189538724487 0.2427477302629888 chrMT 16571 10613 0.6404562186953111 0.9813331998046977 chrX 155270560 10302470 0.06635172823489527 0.3648167423186351 chrY 59373566 539771 0.009091099564408848 0.29561970158516254