BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714149.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 = 727,482 number of mapped reads = 590,243 (81.14%) number of supplementary alignments = 20,320 (2.79%) number of secondary alignments = 0 number of mapped bases = 76,873,106 bp number of sequenced bases = 74,973,403 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 521,580 duplication rate = 43.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2366 >>>>>>> ACTG content number of A's = 21,008,444 bp (28.02%) number of C's = 15,347,586 bp (20.47%) number of T's = 19,867,428 bp (26.5%) number of G's = 18,749,286 bp (25.01%) number of N's = 659 bp (0%) GC percentage = 45.48% >>>>>>> Mismatches and indels general error rate = 0.0481 number of mismatches = 3,390,523 number of insertions = 84,677 mapped reads with insertion percentage = 13.79% number of deletions = 302,272 mapped reads with deletion percentage = 47.21% homopolymer indels = 29.83% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 4.995X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 5726289 0.0229740209955184 3.667878932645844 chr2 243199373 8562659 0.035208392580847646 12.650082259361552 chr3 198022430 3983622 0.020117024116914434 2.7561524674899025 chr4 191154276 3147383 0.016465145671133195 2.448942146728903 chr5 180915260 4611970 0.025492432202789305 4.207010428765194 chr6 171115067 3625329 0.021186497855270686 3.336458509422027 chr7 159138663 3512959 0.022074830426343346 2.927430659793491 chr8 146364022 4153266 0.028376276787474453 4.698042802946551 chr9 141213431 3092240 0.021897633802269133 3.226472015067307 chr10 135534747 3844736 0.02836716107936513 5.010643294850881 chr11 135006516 4069536 0.030143256196612022 4.9610505307192385 chr12 133851895 2393423 0.01788112898961946 2.6777365258946753 chr13 115169878 2879970 0.025006278117269517 3.860110476169943 chr14 107349540 2862764 0.02666768763051989 3.729119717686222 chr15 102531392 1681339 0.01639828512227748 1.9061512116955144 chr16 90354753 1729133 0.019137155961236482 2.582736446349669 chr17 81195210 2141760 0.026377910716654344 3.979139167810619 chr18 78077248 1801696 0.023075813327846802 2.7240529568040173 chr19 59128983 1199417 0.02028475612374392 2.501073657716623 chr20 63025520 1399412 0.022203894549382534 2.833846934156333 chr21 48129895 550076 0.011428988157983723 1.6604512133995482 chr22 51304566 1053650 0.020537158427575433 3.7655755381759337 chrMT 16571 653728 39.45012371009595 311.4978676834351 chrX 155270560 7735035 0.04981649451125828 5.03606098740455 chrY 59373566 461714 0.007776423602382245 1.3048832668765387