BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971303.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,819,028 number of mapped reads = 7,400,721 (83.92%) number of secondary alignments = 0 number of mapped bases = 292,134,527 bp number of sequenced bases = 292,104,580 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 395,947 duplication rate = 4.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.462 >>>>>>> ACTG content number of A's = 85,877,674 bp (29.4%) number of C's = 58,539,098 bp (20.04%) number of T's = 87,770,217 bp (30.05%) number of G's = 59,900,185 bp (20.51%) number of N's = 17,406 bp (0.01%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 802,644 number of insertions = 9,677 mapped reads with insertion percentage = 0.13% number of deletions = 23,817 mapped reads with deletion percentage = 0.32% homopolymer indels = 41.34% >>>>>>> Coverage mean coverageData = 0.0944X std coverageData = 0.7192X There is a 7.48% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 22224332 0.08916460031608106 1.0863604094020662 chr2 243199373 25385280 0.10438053226395448 0.5730689648310414 chr3 198022430 20363328 0.1028334416459792 0.38787281679864144 chr4 191154276 21167088 0.11073300813841068 0.437258834892107 chr5 180915260 18661264 0.10314919813839916 0.3941424364359564 chr6 171115067 17171248 0.10034912939606891 0.41675824520585775 chr7 159138663 16274824 0.10226819613282788 0.8788739222990087 chr8 146364022 16352510 0.11172492923158397 1.940618875272034 chr9 141213431 12128860 0.08589027200960793 0.5323694685619023 chr10 135534747 12828663 0.0946522075257941 0.6227294580327013 chr11 135006516 13203133 0.09779626488546671 0.5496525688722125 chr12 133851895 13341095 0.09967057246369206 0.3928173718082604 chr13 115169878 10579639 0.09186116355875622 0.36148799464360903 chr14 107349540 9532533 0.08879901115552055 0.44088358324966476 chr15 102531392 8384044 0.08177050790454499 0.3404646916476457 chr16 90354753 7704955 0.08527448467486819 0.40711821088977 chr17 81195210 6325660 0.07790681248315018 0.3674157991638584 chr18 78077248 9710683 0.12437276221620926 1.045588347723771 chr19 59128983 4867504 0.0823201034930704 0.9972738593472339 chr20 63025520 5476779 0.08689779949455395 0.376113580423546 chr21 48129895 3976853 0.08262750209615043 0.4168742910950204 chr22 51304566 3097708 0.06037879747389346 0.32442079311137156 chrMT 16571 11656 0.7033975016595256 1.045279843179225 chrX 155270560 10706016 0.06895071415985103 0.385459328858465 chrY 59373566 2658872 0.04478208366329218 0.42105833526785574