BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240050.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 = 1,477,187 number of mapped reads = 1,216,145 (82.33%) number of supplementary alignments = 5,529 (0.37%) number of secondary alignments = 0 number of mapped bases = 76,408,461 bp number of sequenced bases = 76,370,009 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,728 duplication rate = 4.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.905 >>>>>>> ACTG content number of A's = 20,851,564 bp (27.3%) number of C's = 13,470,596 bp (17.64%) number of T's = 24,702,347 bp (32.35%) number of G's = 17,294,066 bp (22.65%) number of N's = 51,436 bp (0.07%) GC percentage = 40.28% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 704,401 number of insertions = 5,379 mapped reads with insertion percentage = 0.44% number of deletions = 22,302 mapped reads with deletion percentage = 1.81% homopolymer indels = 49.18% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2466X There is a 2.08% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 5543610 0.022241108077319494 0.3783923111799923 chr2 243199373 7994726 0.03287313573789518 0.2815104150065643 chr3 198022430 5193229 0.02622545839882886 0.18733778081878297 chr4 191154276 5148948 0.02693608590790823 0.1950053600421925 chr5 180915260 4215044 0.023298443702316766 0.17720160237033183 chr6 171115067 4193013 0.024504054923462703 0.21318731490563494 chr7 159138663 4763328 0.029931934265402242 0.37540953478702854 chr8 146364022 4086270 0.027918541347545095 0.3618525649847909 chr9 141213431 2915523 0.02064621601043034 0.21413961827971054 chr10 135534747 3054244 0.022534767412817024 0.20930947585910695 chr11 135006516 3318984 0.024583880084721243 0.22838048002786898 chr12 133851895 3627042 0.02709742734684481 0.19117623007567777 chr13 115169878 1700655 0.014766491286897082 0.14114848411286576 chr14 107349540 2561223 0.0238587235678886 0.18328778696095385 chr15 102531392 2292356 0.02235760146512007 0.1789666215274939 chr16 90354753 2298462 0.025438196925844068 0.1893611627486158 chr17 81195210 1975819 0.024334181782398247 0.19015089888420567 chr18 78077248 1994814 0.02554923554682665 0.32109357227073393 chr19 59128983 1646447 0.027845007921073157 0.27972491408425765 chr20 63025520 1394387 0.022124164941439595 0.17537135381054475 chr21 48129895 1177896 0.024473271757605122 0.1840074644571278 chr22 51304566 659728 0.012859050401089056 0.1289130429771534 chrMT 16571 21778 1.3142236437149237 1.7933553130649849 chrX 155270560 4455943 0.028697925736855718 0.2091169307972407 chrY 59373566 174992 0.0029473048662766862 0.06892667303783971