BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751204.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,439,056 number of mapped reads = 4,065,149 (91.58%) number of supplementary alignments = 153,405 (3.46%) number of secondary alignments = 0 number of mapped bases = 400,116,651 bp number of sequenced bases = 399,989,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,038 duplication rate = 1.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0971 >>>>>>> ACTG content number of A's = 116,912,531 bp (29.23%) number of C's = 82,957,998 bp (20.74%) number of T's = 117,560,331 bp (29.39%) number of G's = 82,556,501 bp (20.64%) number of N's = 2,253 bp (0%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 1,597,186 number of insertions = 152,433 mapped reads with insertion percentage = 3.65% number of deletions = 57,958 mapped reads with deletion percentage = 1.4% homopolymer indels = 50.68% >>>>>>> Coverage mean coverageData = 0.1292X std coverageData = 1.4066X There is a 10.35% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 48910113 0.19622865051959087 4.051618970231122 chr2 243199373 30368890 0.12487240252876804 0.5743761302007624 chr3 198022430 25763033 0.13010159000674823 0.4666720618919419 chr4 191154276 18773694 0.09821226285306849 0.49608436829272873 chr5 180915260 32744001 0.18099081857439775 0.4896582075856146 chr6 171115067 18285679 0.10686188727027761 0.7932098988239779 chr7 159138663 23045833 0.14481605265214526 0.8012891443990021 chr8 146364022 21228982 0.1450423520064241 0.5396799040056012 chr9 141213431 17665477 0.12509771113768917 0.6627587342199089 chr10 135534747 20310415 0.14985393376651968 1.8633572200337947 chr11 135006516 15086987 0.11175006545609992 0.5934380432072931 chr12 133851895 21239448 0.15867872472033362 0.4589592272940217 chr13 115169878 11538163 0.10018386057507155 0.35963296266596395 chr14 107349540 8623773 0.08033358130831302 0.3462215157341155 chr15 102531392 9846948 0.09603837232600919 0.352429528651492 chr16 90354753 11931829 0.13205535518424802 0.8543402371533182 chr17 81195210 16698169 0.2056546069651153 0.7224074622529307 chr18 78077248 8317585 0.1065302019866274 1.310960731394226 chr19 59128983 8183182 0.13839544644290602 2.7648632111590636 chr20 63025520 7285637 0.11559820529842514 0.40736429081255815 chr21 48129895 5353313 0.11122635941757197 0.46730108737021325 chr22 51304566 4262287 0.08307812213049419 0.33186335450443444 chrMT 16571 1440385 86.92203246635688 30.43922844364085 chrX 155270560 12220440 0.07870416645628121 0.38320684383130577 chrY 59373566 992388 0.016714306834795807 0.7046272500169233