BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472624.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,216,502 number of mapped reads = 19,071,248 (99.24%) number of supplementary alignments = 101,902 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,567,486 number of mapped paired reads (second in pair) = 9,503,762 number of mapped paired reads (both in pair) = 18,967,474 number of mapped paired reads (singletons) = 103,774 number of mapped bases = 1,879,691,907 bp number of sequenced bases = 1,879,413,210 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,386,215 duplication rate = 50.01% >>>>>>> Insert size mean insert size = 22,316.6417 std insert size = 1,465,056.4639 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 54.675 >>>>>>> ACTG content number of A's = 504,641,019 bp (26.85%) number of C's = 437,500,740 bp (23.28%) number of T's = 506,326,631 bp (26.94%) number of G's = 430,602,943 bp (22.91%) number of N's = 341,877 bp (0.02%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 11,656,309 number of insertions = 123,261 mapped reads with insertion percentage = 0.64% number of deletions = 114,871 mapped reads with deletion percentage = 0.59% homopolymer indels = 46.42% >>>>>>> Coverage mean coverageData = 0.6072X std coverageData = 26.6136X There is a 3.81% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 230374137 0.9242670532804811 30.27128159610741 chr2 243199373 112261847 0.4616041793824855 22.251581841003862 chr3 198022430 208494223 1.0528818528284902 39.41147451450065 chr4 191154276 40672751 0.2127744764652819 10.656365001214477 chr5 180915260 75223385 0.4157934770123869 15.730913230073721 chr6 171115067 123112962 0.7194747029494486 23.0591619364435 chr7 159138663 120188474 0.7552437084380934 35.722103573785226 chr8 146364022 104249634 0.7122627034668397 24.120496018158704 chr9 141213431 74058439 0.5244433087954644 20.74053073174753 chr10 135534747 44640619 0.32936660146641217 30.422146290021686 chr11 135006516 52265899 0.38713612163726974 15.776448252467103 chr12 133851895 97183256 0.7260506547180374 28.00604726070648 chr13 115169878 70841972 0.6151085095358007 30.298365458187597 chr14 107349540 32983174 0.3072502592931465 12.934296027479695 chr15 102531392 37115550 0.36199206190431904 16.94482583650771 chr16 90354753 95440070 1.0562816767370278 39.264832485585366 chr17 81195210 74366149 0.9158933020802582 26.74639449020605 chr18 78077248 25882369 0.3314969426176496 12.402430013042473 chr19 59128983 34796762 0.5884891001761353 13.48991035504286 chr20 63025520 104602937 1.6596917724756575 63.48507384271533 chr21 48129895 12443084 0.25853129328455837 12.06636373974344 chr22 51304566 26386284 0.5143067383125315 24.882529038283938 chrMT 16571 1425 0.08599360328284353 0.4057741405614565 chrX 155270560 77776564 0.5009099213656472 24.99141863162487 chrY 59373566 4329941 0.07292708340947553 6.4126168999524635