BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004043.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,039,143 number of mapped reads = 1,898,344 (93.1%) number of supplementary alignments = 19,136 (0.94%) number of secondary alignments = 0 number of mapped bases = 127,007,935 bp number of sequenced bases = 126,956,311 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,142 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0837 >>>>>>> ACTG content number of A's = 35,854,954 bp (28.24%) number of C's = 23,411,963 bp (18.44%) number of T's = 40,055,671 bp (31.55%) number of G's = 27,607,137 bp (21.75%) number of N's = 26,586 bp (0.02%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 927,562 number of insertions = 8,962 mapped reads with insertion percentage = 0.47% number of deletions = 29,206 mapped reads with deletion percentage = 1.52% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.041X std coverageData = 0.3901X There is a 3.42% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 11927594 0.047853818586875256 0.735406363544849 chr2 243199373 8971256 0.036888483261015646 0.3716288887854336 chr3 198022430 8624650 0.04355390447435677 0.23997107770222678 chr4 191154276 10199461 0.05335722126352015 0.2837527903731948 chr5 180915260 10400203 0.05748659897456964 0.27862052719238967 chr6 171115067 7499934 0.043829769823834394 0.26794564305291785 chr7 159138663 9158546 0.05755072857436285 0.6823988389943939 chr8 146364022 8731657 0.05965712666737185 0.5545899727028145 chr9 141213431 4832898 0.03422406753929801 0.3305072080332851 chr10 135534747 5365494 0.039587590036966686 0.327608483986464 chr11 135006516 4574937 0.03388678661998803 0.2638233340036388 chr12 133851895 4403375 0.03289736764653201 0.21643883144219253 chr13 115169878 5278254 0.04583016055639132 0.24649550996786534 chr14 107349540 3342352 0.0311352242403647 0.23807818071360878 chr15 102531392 3514217 0.034274546862681825 0.21962407487464453 chr16 90354753 2058343 0.022780683158970066 0.20826547248515032 chr17 81195210 1905837 0.023472283648259547 0.18683159268337743 chr18 78077248 3255785 0.041699535823803625 0.5985635350171497 chr19 59128983 1187716 0.02008686670629867 0.4648705333872994 chr20 63025520 2212373 0.03510281232110421 0.23191888960523305 chr21 48129895 1158705 0.024074538288521095 0.20612141950138035 chr22 51304566 510510 0.009950576328820324 0.11112098540512955 chrMT 16571 11694 0.7056906644137348 1.0123165917049683 chrX 155270560 7569246 0.0487487518561149 0.27827440871641307 chrY 59373566 312898 0.005269988331170811 0.11519313925542592