BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004096.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,426,248 number of mapped reads = 2,090,156 (86.15%) number of supplementary alignments = 12,264 (0.51%) number of secondary alignments = 0 number of mapped bases = 131,849,621 bp number of sequenced bases = 131,771,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,050 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3976 >>>>>>> ACTG content number of A's = 36,037,227 bp (27.35%) number of C's = 24,140,372 bp (18.32%) number of T's = 41,183,304 bp (31.25%) number of G's = 30,392,963 bp (23.06%) number of N's = 17,784 bp (0.01%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,321,885 number of insertions = 11,565 mapped reads with insertion percentage = 0.55% number of deletions = 48,517 mapped reads with deletion percentage = 2.29% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.379X There is a 3.47% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11402639 0.04574768541900644 0.5180374480488157 chr2 243199373 11108714 0.045677395722562165 0.5305045355174582 chr3 198022430 8651438 0.04368918207902004 0.24698173469187354 chr4 191154276 8686534 0.0454425304093119 0.26396601283302384 chr5 180915260 7313966 0.04042757918817904 0.2400720684310541 chr6 171115067 7907454 0.04621132515466917 0.29686721900091084 chr7 159138663 8085347 0.050806930557158195 0.6715478900360986 chr8 146364022 8361320 0.05712688053898929 0.42999122141672075 chr9 141213431 4639397 0.03285379419752219 0.35606206147887404 chr10 135534747 6236626 0.04601496028173498 0.31050297319743364 chr11 135006516 5679594 0.04206903613452257 0.3996479092371402 chr12 133851895 5743860 0.04291205589580932 0.25070106352753374 chr13 115169878 3770791 0.032741121771440965 0.21595834728434962 chr14 107349540 3235557 0.03014038998210891 0.2428480057831388 chr15 102531392 3389437 0.03305755372949584 0.23295860282009725 chr16 90354753 3822768 0.04230843285023423 0.2652185001010397 chr17 81195210 3281067 0.040409612833072296 0.26905921480126127 chr18 78077248 3877496 0.04966230367135891 0.6488455296175815 chr19 59128983 2403791 0.040653345923436564 0.4166878360834058 chr20 63025520 3068892 0.048692846961040544 0.2712210379730218 chr21 48129895 2001115 0.04157738137596186 0.25601891973642865 chr22 51304566 1535866 0.029936243881295087 0.20428552854157672 chrMT 16571 121806 7.3505521694526585 6.663249163799874 chrX 155270560 7200532 0.04637409693118902 0.29555273486366684 chrY 59373566 323614 0.005450472690153056 0.109142111826844