BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240025.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 = 1,858,299 number of mapped reads = 1,446,656 (77.85%) number of supplementary alignments = 8,598 (0.46%) number of secondary alignments = 0 number of mapped bases = 87,736,519 bp number of sequenced bases = 87,685,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 217,492 duplication rate = 12.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0197 >>>>>>> ACTG content number of A's = 23,623,559 bp (26.94%) number of C's = 15,276,832 bp (17.42%) number of T's = 28,707,963 bp (32.74%) number of G's = 20,022,462 bp (22.83%) number of N's = 54,422 bp (0.06%) GC percentage = 40.26% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 896,613 number of insertions = 6,300 mapped reads with insertion percentage = 0.43% number of deletions = 30,416 mapped reads with deletion percentage = 2.08% homopolymer indels = 48.68% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.346X There is a 1.71% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 5750459 0.02307099166665667 0.42688239104104225 chr2 243199373 7333203 0.030153050600175684 0.40060827889859296 chr3 198022430 5749658 0.029035387556854038 0.25834283247471346 chr4 191154276 4721752 0.024701262764323408 0.24475435769957485 chr5 180915260 4833551 0.0267172100352397 0.2514204180538584 chr6 171115067 4269875 0.02495323804536745 0.2594271953178117 chr7 159138663 6099933 0.03833093030321613 0.6741169930253845 chr8 146364022 4851212 0.03314483937862817 0.41640537587364884 chr9 141213431 3330737 0.0235865453902894 0.2883062124698133 chr10 135534747 3523870 0.025999753406408765 0.3030774506934832 chr11 135006516 4233609 0.03135855309383734 0.2999432658618399 chr12 133851895 5043364 0.03767868956954252 0.2967276398450836 chr13 115169878 1612230 0.01399871240638112 0.18124134284450677 chr14 107349540 3015470 0.028090199548130343 0.26441896563464184 chr15 102531392 1673299 0.01631987011353557 0.20119669624781322 chr16 90354753 2514368 0.027827733644515636 0.25811525120386136 chr17 81195210 2206780 0.027178696871404114 0.2589860464027246 chr18 78077248 4520611 0.05789921027954264 0.5979071867859478 chr19 59128983 1583437 0.0267793714632298 0.3652629900041206 chr20 63025520 2430269 0.03856007852057389 0.32589431277281966 chr21 48129895 2174251 0.045174646651525006 0.32436242795349657 chr22 51304566 920672 0.017945225382083926 0.1942992177234173 chrMT 16571 80453 4.855047975378674 4.75153330964948 chrX 155270560 5048138 0.032511881196280866 0.31061698728503156 chrY 59373566 215318 0.003626496006657239 0.08732999224167237