BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716887.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 = 1,067,149 number of mapped reads = 921,528 (86.35%) number of supplementary alignments = 4,523 (0.42%) number of secondary alignments = 0 number of mapped bases = 52,732,626 bp number of sequenced bases = 52,716,736 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,697 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3182 >>>>>>> ACTG content number of A's = 13,504,360 bp (25.62%) number of C's = 9,663,819 bp (18.33%) number of T's = 17,154,315 bp (32.54%) number of G's = 12,392,791 bp (23.51%) number of N's = 1,451 bp (0%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 267,586 number of insertions = 3,719 mapped reads with insertion percentage = 0.4% number of deletions = 9,971 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.017X std coverageData = 0.1859X There is a 1.58% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5104955 0.020481212762956367 0.31652623227031157 chr2 243199373 4888688 0.020101564982241957 0.2437001628017324 chr3 198022430 4150352 0.020958999442638897 0.15342241907567644 chr4 191154276 2442072 0.012775398233832865 0.12381844567731815 chr5 180915260 2257939 0.012480644253005524 0.11953733217060473 chr6 171115067 3632125 0.021226213820200884 0.169986985926709 chr7 159138663 3794750 0.023845556626298916 0.2554475594119656 chr8 146364022 2973996 0.020319173792586815 0.17088073623271446 chr9 141213431 2114893 0.014976571173318493 0.16140333552440292 chr10 135534747 2771874 0.020451390225415776 0.1896765928805565 chr11 135006516 1694309 0.01254983129851303 0.143532486738444 chr12 133851895 2054754 0.015350951886037923 0.1344376046928801 chr13 115169878 1174319 0.010196407432158607 0.1070880854325798 chr14 107349540 1146504 0.010680101656700159 0.11606077178497168 chr15 102531392 1502099 0.01465013758908101 0.12897275520789325 chr16 90354753 1076250 0.011911382237965944 0.12205076069516575 chr17 81195210 1109983 0.013670547806945755 0.12582077873068542 chr18 78077248 1826328 0.02339129575878494 0.2726510748036992 chr19 59128983 930248 0.01573252156222609 0.2196443602131905 chr20 63025520 780183 0.01237884272910402 0.11777794919117243 chr21 48129895 849092 0.017641675719425525 0.14475429969064899 chr22 51304566 792971 0.015456148678852482 0.13119820725218914 chrMT 16571 69691 4.205600144831332 3.0185752084684547 chrX 155270560 3465918 0.022321797512677224 0.1748455627455473 chrY 59373566 128333 0.0021614500971695047 0.06149523930784956