BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716291.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,129,650 number of mapped reads = 926,926 (82.05%) number of supplementary alignments = 2,915 (0.26%) number of secondary alignments = 0 number of mapped bases = 51,236,357 bp number of sequenced bases = 51,221,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,657 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0761 >>>>>>> ACTG content number of A's = 12,164,231 bp (23.75%) number of C's = 10,841,457 bp (21.17%) number of T's = 15,283,919 bp (29.84%) number of G's = 12,930,871 bp (25.24%) number of N's = 1,282 bp (0%) GC percentage = 46.41% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 271,809 number of insertions = 3,179 mapped reads with insertion percentage = 0.34% number of deletions = 8,729 mapped reads with deletion percentage = 0.93% homopolymer indels = 36.87% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.157X There is a 1.52% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 4186413 0.016795998273560972 0.1660103255238593 chr2 243199373 4320542 0.01776543231466308 0.19748375816437475 chr3 198022430 3324241 0.016787194258751394 0.14531305859238508 chr4 191154276 3240911 0.016954425858619036 0.15823899672473382 chr5 180915260 2977727 0.016459236219211137 0.13879982416073636 chr6 171115067 2762613 0.016144767660933097 0.1400427806246808 chr7 159138663 2731699 0.01716552689650283 0.16558093610265268 chr8 146364022 2507093 0.017129161700680785 0.14769326964504745 chr9 141213431 2056842 0.014565484213750177 0.13913001827770025 chr10 135534747 2515151 0.01855724126596112 0.20870916107114237 chr11 135006516 2259998 0.016739917945886404 0.1575133351992231 chr12 133851895 2456463 0.018352097293803722 0.1473457127657338 chr13 115169878 1524931 0.013240710387832486 0.12462279285228715 chr14 107349540 1571575 0.014639792587839687 0.1331305533304206 chr15 102531392 1485268 0.014485982985581626 0.1329677635306594 chr16 90354753 1689051 0.01869354897135295 0.15733898407411345 chr17 81195210 1601318 0.019721828418203486 0.15874243875313818 chr18 78077248 1266818 0.016225187650056518 0.17520039283923364 chr19 59128983 1279753 0.021643413011179308 0.1805939121967303 chr20 63025520 1134329 0.01799793163150419 0.15116721928965746 chr21 48129895 664547 0.01380736442495875 0.14368774949341417 chr22 51304566 722642 0.014085335016770242 0.13485735928254747 chrMT 16571 4587 0.27680888298835316 0.5697543136274396 chrX 155270560 2763540 0.017798222663716806 0.1522256384925375 chrY 59373566 188305 0.0031715292290175057 0.09978789255627003