BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174066.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,910,206 number of mapped reads = 5,779,124 (97.78%) number of supplementary alignments = 517,792 (8.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,889,504 number of mapped paired reads (second in pair) = 2,889,620 number of mapped paired reads (both in pair) = 5,693,440 number of mapped paired reads (singletons) = 85,684 number of mapped bases = 684,332,835 bp number of sequenced bases = 683,984,394 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,487,936 duplication rate = 66.28% >>>>>>> Insert size mean insert size = 735,498.469 std insert size = 8,062,066.7602 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.9418 >>>>>>> ACTG content number of A's = 205,752,406 bp (30.08%) number of C's = 134,510,887 bp (19.67%) number of T's = 205,288,383 bp (30.01%) number of G's = 138,424,335 bp (20.24%) number of N's = 8,383 bp (0%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 6,529,140 number of insertions = 67,954 mapped reads with insertion percentage = 1.14% number of deletions = 138,184 mapped reads with deletion percentage = 2.33% homopolymer indels = 44.24% >>>>>>> Coverage mean coverageData = 0.2211X std coverageData = 3.0561X There is a 4.5% of reference with a coverageData >= 1X There is a 3.6% of reference with a coverageData >= 2X There is a 2.8% of reference with a coverageData >= 3X There is a 2.31% of reference with a coverageData >= 4X There is a 1.77% of reference with a coverageData >= 5X There is a 1.44% of reference with a coverageData >= 6X There is a 1.07% of reference with a coverageData >= 7X There is a 0.88% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 51480519 0.20654118651122638 2.0977226609556494 chr2 243199373 58836435 0.24192675447399284 9.256846598735619 chr3 198022430 55840009 0.28198830304223615 1.571122974423531 chr4 191154276 32027912 0.16755006830189872 1.36601055415398 chr5 180915260 45607218 0.2520916035496398 1.4531043324731188 chr6 171115067 40489573 0.23662190425346938 1.669013982499243 chr7 159138663 36825902 0.23140763725028907 1.8484979447170065 chr8 146364022 42086958 0.28754988708905527 2.0415552752542574 chr9 141213431 28346896 0.20073795955003743 1.5921662434700132 chr10 135534747 27928077 0.2060584286920903 2.55864973772698 chr11 135006516 23882890 0.17690175783811798 1.2327184154786983 chr12 133851895 29193917 0.21810611646551586 1.3563837466482527 chr13 115169878 23362676 0.202854048347607 1.3223115622670776 chr14 107349540 20620381 0.1920863470863499 1.2705627422966357 chr15 102531392 22202220 0.21654070589424945 1.3492819392812305 chr16 90354753 23555897 0.2607045696865554 1.842105501516386 chr17 81195210 27743549 0.3416894789729591 1.865915212892437 chr18 78077248 13531764 0.173312512244284 2.031297449883898 chr19 59128983 10720254 0.18130286462055334 1.5858115839684952 chr20 63025520 30151759 0.47840555698707443 2.217130509783694 chr21 48129895 8536844 0.17737092507681557 1.282814845337443 chr22 51304566 5439959 0.10603264824421281 0.930002558635321 chrMT 16571 1078804 65.10192504978578 60.43844278977217 chrX 155270560 23718432 0.15275549981915437 1.1246956811367568 chrY 59373566 1123990 0.018930815103812358 0.6867308288665633