BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004044.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 = 2,984,118 number of mapped reads = 2,517,462 (84.36%) number of supplementary alignments = 29,729 (1%) number of secondary alignments = 0 number of mapped bases = 165,519,121 bp number of sequenced bases = 165,448,301 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,566 duplication rate = 5.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5229 >>>>>>> ACTG content number of A's = 45,698,553 bp (27.62%) number of C's = 31,051,532 bp (18.77%) number of T's = 51,692,806 bp (31.24%) number of G's = 36,986,954 bp (22.36%) number of N's = 18,456 bp (0.01%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,244,065 number of insertions = 11,550 mapped reads with insertion percentage = 0.46% number of deletions = 40,696 mapped reads with deletion percentage = 1.6% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.0535X std coverageData = 0.4918X There is a 3.9% of reference with a coverageData >= 1X There is a 0.97% 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 0.01% 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 14061084 0.05641343617755721 0.9451616364071647 chr2 243199373 11858759 0.048761470285534 0.4651035963291468 chr3 198022430 11859569 0.059890028619485176 0.3160267251967937 chr4 191154276 11609601 0.06073419461461589 0.3434113499285965 chr5 180915260 10948931 0.06051966539472679 0.3229304008581956 chr6 171115067 9548797 0.055803367683571664 0.3513812380735468 chr7 159138663 9507276 0.05974208794251338 0.7139302474767132 chr8 146364022 13047621 0.08914500176826243 0.7167418155550723 chr9 141213431 6696723 0.047422705847292954 0.419124211798192 chr10 135534747 7939270 0.05857737720940299 0.4711887445696739 chr11 135006516 5194278 0.03847427630826352 0.38214037308424087 chr12 133851895 7151838 0.053430980562509035 0.31071873089039237 chr13 115169878 5412031 0.04699172295728229 0.282872162118401 chr14 107349540 4441804 0.04137701940781488 0.31402284417964127 chr15 102531392 5451156 0.05316572703899309 0.30695507987819703 chr16 90354753 3808968 0.04215570153791467 0.2997555548234968 chr17 81195210 3789032 0.046665708482064396 0.30815213002371755 chr18 78077248 2880247 0.03688970953484426 0.6987962137781693 chr19 59128983 2730202 0.04617366748891994 0.6642038768251066 chr20 63025520 3357684 0.05327499082911176 0.31757823017039616 chr21 48129895 2379932 0.04944810288906718 0.3131238963182828 chr22 51304566 1189784 0.023190606465709116 0.19111685474411594 chrMT 16571 113041 6.821616076277834 5.5475225802152535 chrX 155270560 10106359 0.0650887006525899 0.37327151679524606 chrY 59373566 435134 0.0073287496324542815 0.15727773674922768