BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716388.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 = 928,265 number of mapped reads = 812,322 (87.51%) number of supplementary alignments = 2,825 (0.3%) number of secondary alignments = 0 number of mapped bases = 45,770,326 bp number of sequenced bases = 45,755,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,589 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.963 >>>>>>> ACTG content number of A's = 11,010,539 bp (24.06%) number of C's = 8,729,669 bp (19.08%) number of T's = 14,646,040 bp (32.01%) number of G's = 11,369,406 bp (24.85%) number of N's = 327 bp (0%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 240,828 number of insertions = 2,988 mapped reads with insertion percentage = 0.37% number of deletions = 8,955 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.12% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1533X There is a 1.39% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 3851818 0.015453594396460902 0.180917762419696 chr2 243199373 3567955 0.014670905422112251 0.2210254891105117 chr3 198022430 2637209 0.013317728703763508 0.12188934967606176 chr4 191154276 2819377 0.014749222769152179 0.13259892146137836 chr5 180915260 2614453 0.014451257456115089 0.1254651968927481 chr6 171115067 2465139 0.014406323436147209 0.13864000437692245 chr7 159138663 2633907 0.016551018780395308 0.2028966993824831 chr8 146364022 2368252 0.016180561094447102 0.14558550846361845 chr9 141213431 1522392 0.010780787558373254 0.12115408838964821 chr10 135534747 2024199 0.014934908167866355 0.1780289791895506 chr11 135006516 1602802 0.011872034383881146 0.13121332781983414 chr12 133851895 2304162 0.017214265065130383 0.13746017980002478 chr13 115169878 1373810 0.011928553054471413 0.1139138656595875 chr14 107349540 1529918 0.014251742485342741 0.12854557914954964 chr15 102531392 1680499 0.016390092509423845 0.1366801546301214 chr16 90354753 1593909 0.017640566180287164 0.14471228793861238 chr17 81195210 2038294 0.025103623723616207 0.17105434311470957 chr18 78077248 835676 0.010703194866704319 0.1529648073304515 chr19 59128983 1211405 0.020487499336831146 0.1815338810766046 chr20 63025520 1453146 0.023056469823652385 0.1643377153303167 chr21 48129895 567468 0.011790343610764161 0.11916581129064312 chr22 51304566 428488 0.008351849229169973 0.09548761252531221 chrMT 16571 17435 1.052139279464124 1.2462739334120259 chrX 155270560 2485192 0.016005558297722374 0.13716730078515924 chrY 59373566 143421 0.0024155699187749648 0.07559462028574553