BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082894.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,599,924 number of mapped reads = 3,003,854 (83.44%) number of supplementary alignments = 22,484 (0.62%) number of secondary alignments = 0 number of mapped bases = 203,466,598 bp number of sequenced bases = 203,390,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,651 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2284 >>>>>>> ACTG content number of A's = 57,666,468 bp (28.35%) number of C's = 36,525,632 bp (17.96%) number of T's = 66,559,644 bp (32.73%) number of G's = 42,627,813 bp (20.96%) number of N's = 11,000 bp (0.01%) GC percentage = 38.92% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,797,857 number of insertions = 16,558 mapped reads with insertion percentage = 0.55% number of deletions = 44,378 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 0.0657X std coverageData = 0.4673X There is a 5.15% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 19136849 0.07677753789829073 0.8271358719289281 chr2 243199373 21068479 0.08663048239026504 0.5742529061393243 chr3 198022430 15314694 0.0773381783063666 0.3369523764206705 chr4 191154276 12171586 0.06367414977418553 0.31447481101550606 chr5 180915260 11782203 0.06512553446293032 0.3140816101510267 chr6 171115067 14574342 0.0851727568794395 0.47689402166343514 chr7 159138663 10319158 0.06484381485597877 0.41745148032926377 chr8 146364022 15520410 0.10603978893118966 0.6781095759787679 chr9 141213431 6041155 0.04278031457220241 0.4200274850176956 chr10 135534747 7565109 0.05581674933882453 0.37915141373960265 chr11 135006516 8026023 0.059449152809779936 0.37102340886120344 chr12 133851895 6535268 0.048824620674963175 0.275679413836104 chr13 115169878 4829186 0.04193098129356358 0.2464632529860315 chr14 107349540 4256028 0.03964644841514924 0.27380111920773725 chr15 102531392 4023319 0.039239874944836405 0.23793165038856837 chr16 90354753 8082046 0.08944793418891865 0.40577868948866547 chr17 81195210 4803742 0.05916287426314927 0.3522699199981152 chr18 78077248 7655303 0.09804780773010852 0.8630943579268219 chr19 59128983 2627583 0.04443815649594379 0.5840182979586297 chr20 63025520 3802623 0.06033465491439023 0.3113576984397346 chr21 48129895 4132497 0.08586133420818808 0.3675530104073994 chr22 51304566 2434210 0.0474462643344454 0.2588429284487741 chrMT 16571 106174 6.407217428036932 4.668930074546865 chrX 155270560 8322079 0.053597275620053154 0.31709502164272785 chrY 59373566 336532 0.005668044260639491 0.1123214197292903