BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818845.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,848,706 number of mapped reads = 1,824,484 (98.69%) number of supplementary alignments = 28,628 (1.55%) number of secondary alignments = 0 number of mapped bases = 169,068,386 bp number of sequenced bases = 168,962,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 426,099 duplication rate = 20.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3736 >>>>>>> ACTG content number of A's = 49,659,741 bp (29.39%) number of C's = 35,694,014 bp (21.13%) number of T's = 46,757,193 bp (27.67%) number of G's = 36,848,872 bp (21.81%) number of N's = 2,423 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,026,344 number of insertions = 24,583 mapped reads with insertion percentage = 1.31% number of deletions = 54,756 mapped reads with deletion percentage = 2.93% homopolymer indels = 39.98% >>>>>>> Coverage mean coverageData = 0.0546X std coverageData = 0.6329X There is a 3.7% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 16031492 0.06431876452576622 0.9731426680078081 chr2 243199373 12640505 0.05197589469114297 0.8682852980458141 chr3 198022430 10463992 0.052842458301314656 0.31403099734740536 chr4 191154276 8459488 0.0442547672854569 0.3839026067490892 chr5 180915260 8578898 0.04741942719480933 0.3112151374755496 chr6 171115067 8360200 0.04885718216736577 0.34122860230098573 chr7 159138663 14977369 0.09411521196454943 1.3300641710766343 chr8 146364022 15184170 0.10374250305857269 0.5534756720757162 chr9 141213431 6172211 0.04370838493400815 0.5073606194339524 chr10 135534747 7770875 0.05733492828964369 0.853643888895948 chr11 135006516 7519193 0.05569503771210569 0.3992784109326812 chr12 133851895 6479451 0.04840761499865205 0.3007066175767343 chr13 115169878 5190018 0.045064022729971114 0.2881329654305912 chr14 107349540 4048478 0.03771304469492836 0.29617794617206294 chr15 102531392 4710886 0.04594579189951893 0.29363988539617414 chr16 90354753 4248426 0.047019396976271964 0.6820818505096851 chr17 81195210 4235338 0.05216241204376465 0.40425362505730433 chr18 78077248 3227264 0.04133424374793538 0.6182887854792419 chr19 59128983 2945334 0.04981201858317096 0.8643140745449664 chr20 63025520 7021472 0.11140680790892324 0.5000658714913641 chr21 48129895 1633463 0.03393863626754224 0.3180494684136374 chr22 51304566 1603160 0.031247901015281954 0.2717179547478951 chrMT 16571 201309 12.148271075976103 8.199736718079285 chrX 155270560 6743397 0.04342997796877914 0.33671711355805234 chrY 59373566 621997 0.010475991959115274 0.7837707595727506