BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231772.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 = 2,323,874 number of mapped reads = 1,759,224 (75.7%) number of supplementary alignments = 9,292 (0.4%) number of secondary alignments = 0 number of mapped bases = 110,411,600 bp number of sequenced bases = 110,340,829 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,450 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8435 >>>>>>> ACTG content number of A's = 28,456,666 bp (25.79%) number of C's = 20,468,967 bp (18.55%) number of T's = 34,303,008 bp (31.09%) number of G's = 27,087,075 bp (24.55%) number of N's = 25,113 bp (0.02%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 979,655 number of insertions = 9,041 mapped reads with insertion percentage = 0.51% number of deletions = 40,156 mapped reads with deletion percentage = 2.25% homopolymer indels = 45.53% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.3554X There is a 3.05% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 9445099 0.03789398382281262 0.5667562007889422 chr2 243199373 7299664 0.030015143172264676 0.4461424202923788 chr3 198022430 9214068 0.04653042587145305 0.24655082359264777 chr4 191154276 4745230 0.024824085023345228 0.20458810108953887 chr5 180915260 6138042 0.033927718424637036 0.21451268407450474 chr6 171115067 7099215 0.041487959678033495 0.29749433928896707 chr7 159138663 8092251 0.05085031410625839 0.6457247273463773 chr8 146364022 4500517 0.030748792896658717 0.3644250440529895 chr9 141213431 4940910 0.0349889522902393 0.3141926372428566 chr10 135534747 4596789 0.033915944816719217 0.2825752519933696 chr11 135006516 5113305 0.03787450525721292 0.35912210521340093 chr12 133851895 4566706 0.034117604386549774 0.21263065684342286 chr13 115169878 4439163 0.038544479486207324 0.23311188012918416 chr14 107349540 4820199 0.04490190642642716 0.26205691828958116 chr15 102531392 3291598 0.03210331914736903 0.22114355450268938 chr16 90354753 3477485 0.03848701794359396 0.25601507774890375 chr17 81195210 3144308 0.038725289336649295 0.256643208941652 chr18 78077248 2816874 0.03607803902104746 0.5848158644868718 chr19 59128983 3439670 0.05817231796460967 0.451775411654588 chr20 63025520 2404439 0.0381502445358642 0.24763360807064944 chr21 48129895 1599813 0.03323948660183032 0.2229361259832304 chr22 51304566 1154342 0.022499790759364383 0.17001864877934425 chrMT 16571 57103 3.445959809305413 3.3752129872914174 chrX 155270560 3665192 0.023605195988215668 0.214923098012398 chrY 59373566 349618 0.005888445373148044 0.11722321831411274