BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006185.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,859,340 number of mapped reads = 1,665,196 (89.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 833,748 number of mapped paired reads (second in pair) = 831,448 number of mapped paired reads (both in pair) = 1,551,680 number of mapped paired reads (singletons) = 113,516 number of mapped bases = 64,492,258 bp number of sequenced bases = 64,483,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,962 duplication rate = 1.62% >>>>>>> Insert size mean insert size = 66,529.0877 std insert size = 2,435,057.1924 median insert size = 120 >>>>>>> Mapping quality mean mapping quality = 48.2492 >>>>>>> ACTG content number of A's = 17,826,086 bp (27.64%) number of C's = 14,050,689 bp (21.79%) number of T's = 18,163,016 bp (28.17%) number of G's = 14,441,522 bp (22.4%) number of N's = 2,494 bp (0%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 184,179 number of insertions = 1,864 mapped reads with insertion percentage = 0.11% number of deletions = 6,236 mapped reads with deletion percentage = 0.37% homopolymer indels = 43.68% >>>>>>> Coverage mean coverageData = 0.0208X std coverageData = 0.1722X There is a 1.92% of reference with a coverageData >= 1X There is a 0.14% 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 5436146 0.021809959703169606 0.1983240290124714 chr2 243199373 5500169 0.022615884786841123 0.1696927886667946 chr3 198022430 4358530 0.022010284390510712 0.15765195601759274 chr4 191154276 4060805 0.02124360011700706 0.16019798352647255 chr5 180915260 3744961 0.020700083563984596 0.15295782786261783 chr6 171115067 3557541 0.02079034337753554 0.1575361993866971 chr7 159138663 3421864 0.021502405106922383 0.18442549935554453 chr8 146364022 3150542 0.021525385521313428 0.28574859595103674 chr9 141213431 2667788 0.018891885715884914 0.149806058746381 chr10 135534747 3090257 0.022800477873028382 0.1839980928429758 chr11 135006516 3051206 0.02260043507825948 0.16682278914291104 chr12 133851895 2844343 0.021249927018216663 0.15507375028723702 chr13 115169878 2024791 0.017580907743950203 0.14108970522012618 chr14 107349540 1924519 0.01792759428685023 0.14843874437508328 chr15 102531392 1898579 0.0185170508559954 0.14440583182960495 chr16 90354753 2035327 0.022525953891988394 0.1725629825121098 chr17 81195210 1832391 0.022567722898924704 0.1618824689458432 chr18 78077248 1694884 0.02170778355302687 0.18862358426230935 chr19 59128983 1389802 0.0235045815010889 0.18031385974016473 chr20 63025520 1473379 0.023377498511713984 0.1639315496996933 chr21 48129895 870358 0.0180835216864695 0.14846540554437632 chr22 51304566 884915 0.017248269871340496 0.14163188322157516 chrMT 16571 4179 0.252187556574739 0.5020691121172806 chrX 155270560 3401062 0.021904100816020757 0.16035302026128553 chrY 59373566 173920 0.002929249693373647 0.09237953263001687