BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716721.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,251,767 number of mapped reads = 2,053,394 (91.19%) number of supplementary alignments = 11,691 (0.52%) number of secondary alignments = 0 number of mapped bases = 119,046,731 bp number of sequenced bases = 119,013,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,525 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1268 >>>>>>> ACTG content number of A's = 31,349,693 bp (26.34%) number of C's = 22,885,760 bp (19.23%) number of T's = 35,716,916 bp (30.01%) number of G's = 29,059,301 bp (24.42%) number of N's = 1,446 bp (0%) GC percentage = 43.65% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 599,829 number of insertions = 8,845 mapped reads with insertion percentage = 0.43% number of deletions = 21,262 mapped reads with deletion percentage = 1.03% homopolymer indels = 39.88% >>>>>>> Coverage mean coverageData = 0.0385X std coverageData = 0.3542X There is a 3.38% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 9792639 0.03928832337793854 0.46860073017754844 chr2 243199373 11738204 0.04826576588254609 0.43678288588578357 chr3 198022430 8948778 0.04519072915123807 0.25307100505418745 chr4 191154276 6677942 0.03493482928940601 0.2267860461785906 chr5 180915260 6010953 0.033225240369441474 0.2036924378531838 chr6 171115067 6619447 0.038684185536975536 0.2397648361403552 chr7 159138663 6699355 0.04209759510170071 0.851113159932061 chr8 146364022 8399747 0.05738942456773974 0.35522701982677146 chr9 141213431 4989574 0.035333565402854636 0.2501501892064199 chr10 135534747 5604102 0.04134808323359323 0.4303661779030518 chr11 135006516 4332243 0.03208914005306233 0.2430457702849035 chr12 133851895 5659870 0.04228457131667803 0.25225587854617204 chr13 115169878 3108588 0.02699132840967323 0.18372467747368695 chr14 107349540 3833289 0.035708480911981554 0.2143982706342571 chr15 102531392 2838394 0.02768317043818151 0.19865618241581706 chr16 90354753 3647927 0.04037338246057737 0.2355087959400098 chr17 81195210 5044493 0.06212796296727356 0.2931029654757088 chr18 78077248 2756245 0.035301513188579596 0.4004085083355926 chr19 59128983 2430996 0.04111344177862826 0.4100061782991337 chr20 63025520 2664396 0.042274875320346426 0.242709787910438 chr21 48129895 952512 0.01979044417196422 0.16854961179700012 chr22 51304566 1810413 0.03528756095510095 0.20809380851399104 chrMT 16571 57369 3.4620119485848773 2.5330154125816566 chrX 155270560 4162420 0.02680752874208736 0.21607368613675157 chrY 59373566 266835 0.004494171699237334 0.11289770160285124