BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236096.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 = 1,773,762 number of mapped reads = 1,559,117 (87.9%) number of supplementary alignments = 6,969 (0.39%) number of secondary alignments = 0 number of mapped bases = 102,666,989 bp number of sequenced bases = 102,615,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,612 duplication rate = 2.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4602 >>>>>>> ACTG content number of A's = 28,457,656 bp (27.73%) number of C's = 18,021,047 bp (17.56%) number of T's = 33,086,882 bp (32.24%) number of G's = 23,006,057 bp (22.42%) number of N's = 44,145 bp (0.04%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 821,640 number of insertions = 7,662 mapped reads with insertion percentage = 0.49% number of deletions = 29,364 mapped reads with deletion percentage = 1.86% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0332X std coverageData = 0.3386X There is a 2.93% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 7975936 0.0319996635033459 0.5240384694525813 chr2 243199373 7809504 0.03211153015595974 0.32717826537185685 chr3 198022430 7972403 0.04026010083807173 0.22017202778454506 chr4 191154276 6615239 0.034606806284574035 0.2210727693943735 chr5 180915260 5397177 0.02983262440105937 0.18945055852467182 chr6 171115067 11961938 0.06990581372942455 0.44403007579721454 chr7 159138663 4721233 0.0296674165221559 0.4422986269375834 chr8 146364022 6943176 0.047437723459116204 0.6727352417769066 chr9 141213431 4900247 0.034700998094154376 0.31684411812192653 chr10 135534747 3888006 0.02868641500470724 0.30293599669233506 chr11 135006516 3950638 0.029262572778339085 0.2603605963427273 chr12 133851895 3891517 0.029073305237852627 0.1948907359333097 chr13 115169878 4743945 0.04119084853072433 0.22360500366387726 chr14 107349540 3079227 0.028684119186724043 0.20882798797029767 chr15 102531392 2116471 0.02064217561778543 0.16929404456168215 chr16 90354753 2056181 0.022756755253373333 0.19273476769388767 chr17 81195210 2320606 0.028580577598112007 0.20974013092753205 chr18 78077248 2569432 0.03290884432811976 0.5302528916287899 chr19 59128983 1313185 0.022208821010839982 0.35498223952341706 chr20 63025520 1138985 0.018071806468236994 0.15523777531816538 chr21 48129895 1708171 0.035490852410959964 0.22593258444433628 chr22 51304566 757224 0.014759388082534408 0.12989874666898082 chrMT 16571 62589 3.7770200953472934 2.835738921323136 chrX 155270560 4521550 0.02912045915207622 0.2119140686341441 chrY 59373566 252409 0.0042512016205999825 0.11588279119935231