BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472815.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 = 1,749,167 number of mapped reads = 1,336,037 (76.38%) number of supplementary alignments = 13,647 (0.78%) number of secondary alignments = 0 number of mapped bases = 83,977,102 bp number of sequenced bases = 83,939,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,601 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2565 >>>>>>> ACTG content number of A's = 22,277,993 bp (26.54%) number of C's = 16,996,493 bp (20.25%) number of T's = 24,546,662 bp (29.24%) number of G's = 20,116,906 bp (23.97%) number of N's = 1,641 bp (0%) GC percentage = 44.21% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 762,453 number of insertions = 6,689 mapped reads with insertion percentage = 0.49% number of deletions = 20,607 mapped reads with deletion percentage = 1.52% homopolymer indels = 44.91% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.24X There is a 2.28% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6494484 0.02605603939498309 0.27029262914196944 chr2 243199373 7677675 0.03156946872556288 0.31911976494017463 chr3 198022430 5116165 0.025836290363672437 0.19158642261088593 chr4 191154276 4010115 0.020978421638865145 0.18362575733868783 chr5 180915260 4746786 0.026237620861833323 0.19266043731060958 chr6 171115067 5664325 0.03310243276239374 0.22921784942463208 chr7 159138663 4739198 0.029780305493706454 0.3066795844445645 chr8 146364022 4765862 0.032561704269099684 0.2501214171598499 chr9 141213431 3608021 0.02555012631907513 0.2509521708165596 chr10 135534747 4039543 0.029804482536127802 0.23607416371689627 chr11 135006516 3331948 0.024679905079544456 0.24905107258288325 chr12 133851895 3415666 0.025518249106596513 0.19890838174669165 chr13 115169878 3341166 0.02901076269265476 0.2013151321085809 chr14 107349540 2344609 0.02184088539177718 0.19922478784554293 chr15 102531392 2183257 0.021293546858312428 0.19345708866716263 chr16 90354753 3222971 0.03567018770999241 0.2338591249343993 chr17 81195210 2312287 0.028478120815254988 0.21468288973083052 chr18 78077248 1682620 0.021550708344638375 0.3675552077737965 chr19 59128983 1863515 0.03151610099568261 0.25612846090378616 chr20 63025520 2985733 0.04737339731588093 0.26329688718381283 chr21 48129895 1287899 0.02675881590849097 0.2068419899227719 chr22 51304566 1006348 0.019615174212759153 0.17352477161469776 chrMT 16571 84502 5.099390501478487 4.211089387888539 chrX 155270560 3685108 0.023733462415540977 0.2026913094738683 chrY 59373566 367299 0.006186237828463933 0.10639369191408954