BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238321.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 = 2,440,545 number of mapped reads = 2,156,865 (88.38%) number of supplementary alignments = 32,401 (1.33%) number of secondary alignments = 0 number of mapped bases = 139,596,690 bp number of sequenced bases = 139,518,917 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,130 duplication rate = 6.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3614 >>>>>>> ACTG content number of A's = 39,351,777 bp (28.21%) number of C's = 25,870,697 bp (18.54%) number of T's = 44,096,459 bp (31.61%) number of G's = 30,157,447 bp (21.62%) number of N's = 42,537 bp (0.03%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,252,021 number of insertions = 10,809 mapped reads with insertion percentage = 0.5% number of deletions = 44,760 mapped reads with deletion percentage = 2.05% homopolymer indels = 45.21% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.4687X There is a 3.16% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 9005906 0.03613193003840099 0.9105926554072683 chr2 243199373 10925640 0.04492462240023949 0.5083470004416863 chr3 198022430 8034031 0.04057131810775173 0.26964154103678983 chr4 191154276 6861894 0.03589715147151613 0.2800901174999428 chr5 180915260 9759927 0.05394750558908076 0.3155938288294294 chr6 171115067 11694279 0.06834160898291908 0.4532687051979348 chr7 159138663 11169727 0.07018864422657617 0.6135579831787803 chr8 146364022 8404441 0.05742149529069378 0.6881155300698834 chr9 141213431 5944596 0.042096534004616035 0.37334168742030943 chr10 135534747 6318594 0.04661973508535047 0.40441377179473054 chr11 135006516 7349178 0.054435728124411414 0.4038546727367805 chr12 133851895 5938565 0.04436668603010813 0.28805946964536405 chr13 115169878 2429984 0.02109912802026238 0.19533646261436097 chr14 107349540 3355688 0.0312594539296582 0.2540480990693726 chr15 102531392 5295352 0.05164615340441296 0.3109814352874428 chr16 90354753 3173805 0.03512604367365157 0.26985074753919086 chr17 81195210 4456768 0.05488954336099383 0.37887040288826473 chr18 78077248 4288259 0.05492328571826712 0.6541875853947625 chr19 59128983 3132225 0.052972752803815346 0.6353100733575351 chr20 63025520 2530056 0.04014335780172857 0.2729254582045156 chr21 48129895 2577270 0.05354821571914919 0.33038197249252294 chr22 51304566 2377393 0.04633881904390342 0.2858623261818242 chrMT 16571 4665 0.2815159012733088 0.6786863740086341 chrX 155270560 4243633 0.0273305705859501 0.25396643666705493 chrY 59373566 324814 0.005470683704596756 0.19993979547783822