BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714165.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 798,096 number of mapped reads = 725,433 (90.9%) number of supplementary alignments = 25,716 (3.22%) number of secondary alignments = 0 number of mapped bases = 93,424,079 bp number of sequenced bases = 91,798,131 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 649,505 duplication rate = 42.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9307 >>>>>>> ACTG content number of A's = 26,920,932 bp (29.33%) number of C's = 18,611,822 bp (20.27%) number of T's = 25,433,897 bp (27.71%) number of G's = 20,830,904 bp (22.69%) number of N's = 576 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0399 number of mismatches = 3,336,649 number of insertions = 110,869 mapped reads with insertion percentage = 14.87% number of deletions = 293,379 mapped reads with deletion percentage = 38.72% homopolymer indels = 27.28% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 6.3533X There is a 0.07% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6179950 0.024794120773725174 4.933085780379725 chr2 243199373 12668513 0.05209105946173636 12.42536181386106 chr3 198022430 5603072 0.028295138081074957 4.700109323132809 chr4 191154276 4883581 0.025547851202658945 4.267568292111084 chr5 180915260 6708144 0.037078928554727775 6.7977564179496826 chr6 171115067 4344025 0.025386572183032835 5.220489177846974 chr7 159138663 2635088 0.016558439981363925 2.4448558558145463 chr8 146364022 5036315 0.0344095149284706 7.928052901272541 chr9 141213431 3189420 0.022585811968551348 4.5624854306283575 chr10 135534747 3787549 0.02794522499828033 3.6343389904159316 chr11 135006516 5108094 0.03783590712021633 10.422726419980288 chr12 133851895 3302731 0.02467451805594534 3.914305137130435 chr13 115169878 3378985 0.029339138485498788 7.161167422970057 chr14 107349540 3154088 0.02938147662300183 4.572363812320215 chr15 102531392 2279009 0.022227426698742177 5.216032942382198 chr16 90354753 2206300 0.024418195244250183 5.376240187701468 chr17 81195210 937917 0.011551383388256524 1.9495974124561748 chr18 78077248 2289599 0.029324791263134684 6.179905480131723 chr19 59128983 836176 0.01414155897117324 4.289357763916991 chr20 63025520 999372 0.01585662442769215 1.7248174762844661 chr21 48129895 1197012 0.024870446943630355 6.826420633869849 chr22 51304566 437005 0.008517857845245197 1.3720732913857243 chrMT 16571 7371 0.44481322792830846 3.0629585970117237 chrX 155270560 11808105 0.07604857611127312 7.246904425905985 chrY 59373566 446658 0.0075228427411619505 2.0678692350880468