BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716380.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 = 1,485,138 number of mapped reads = 1,303,146 (87.75%) number of supplementary alignments = 4,955 (0.33%) number of secondary alignments = 0 number of mapped bases = 74,061,394 bp number of sequenced bases = 74,039,261 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,440 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.22 >>>>>>> ACTG content number of A's = 18,606,134 bp (25.13%) number of C's = 14,307,046 bp (19.32%) number of T's = 23,425,423 bp (31.64%) number of G's = 17,700,103 bp (23.91%) number of N's = 555 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 379,341 number of insertions = 5,676 mapped reads with insertion percentage = 0.43% number of deletions = 13,798 mapped reads with deletion percentage = 1.05% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0239X std coverageData = 0.2111X There is a 2.19% of reference with a coverageData >= 1X There is a 0.14% 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 6249634 0.025073694801346153 0.24493387894267613 chr2 243199373 5883079 0.02419035430654667 0.323819599167157 chr3 198022430 4207620 0.021248199004526912 0.1584391423023948 chr4 191154276 4510524 0.023596249554992954 0.17680437930931026 chr5 180915260 4201501 0.02322358545100065 0.16299133363602786 chr6 171115067 3946291 0.023062206439132562 0.18987694246617184 chr7 159138663 4242095 0.026656595701071085 0.28556799354199014 chr8 146364022 3817527 0.02608241388720515 0.20111469091929635 chr9 141213431 2453557 0.017374813306533145 0.16216158671276282 chr10 135534747 3267834 0.024110673257832546 0.25645071727553614 chr11 135006516 2635056 0.019517991264954945 0.18047743762754603 chr12 133851895 3711130 0.02772564407847943 0.17918811414430777 chr13 115169878 2229411 0.019357587580322 0.1491919874760797 chr14 107349540 2466119 0.02297279522576436 0.16772244603540473 chr15 102531392 2704076 0.026373152136664642 0.1780330783336856 chr16 90354753 2563481 0.02837129110407728 0.1902839412810805 chr17 81195210 3320599 0.040896488844600565 0.2264062015776926 chr18 78077248 1371259 0.017562850063567816 0.23494085587465377 chr19 59128983 1998018 0.033790839933776635 0.24879630824586016 chr20 63025520 2391868 0.037950785650003364 0.21846870098245902 chr21 48129895 918908 0.019092250253195026 0.15795184850556146 chr22 51304566 695733 0.013560839789581301 0.12580821576759993 chrMT 16571 5010 0.3023354052259972 0.6565428209097578 chrX 155270560 4035293 0.025988783707613344 0.18375655261273757 chrY 59373566 235771 0.003970975905338076 0.11649645032984975