BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085101.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,566,160 number of mapped reads = 1,228,199 (78.42%) number of supplementary alignments = 5,852 (0.37%) number of secondary alignments = 0 number of mapped bases = 77,569,487 bp number of sequenced bases = 77,544,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,238 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4922 >>>>>>> ACTG content number of A's = 23,289,022 bp (30.03%) number of C's = 14,598,733 bp (18.83%) number of T's = 22,458,447 bp (28.96%) number of G's = 17,196,781 bp (22.18%) number of N's = 1,613 bp (0%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 694,104 number of insertions = 5,776 mapped reads with insertion percentage = 0.47% number of deletions = 15,654 mapped reads with deletion percentage = 1.26% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2109X There is a 2.31% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 8579698 0.03442197241305971 0.3353984794552926 chr2 243199373 5963540 0.02452119808713487 0.21284848405318374 chr3 198022430 3944103 0.019917455815485145 0.151988439232845 chr4 191154276 6115269 0.0319912749427588 0.19224538375760306 chr5 180915260 4128850 0.02282201070269031 0.16007322678016936 chr6 171115067 5390949 0.03150481774933355 0.20488069268939962 chr7 159138663 6932998 0.04356576754701025 0.251190831232679 chr8 146364022 4174909 0.028524147826437838 0.2834553954423439 chr9 141213431 2149490 0.015221569115475992 0.1677918877591417 chr10 135534747 4526137 0.03339466151805338 0.2852911042371608 chr11 135006516 4262669 0.03157380196375114 0.23772801919623773 chr12 133851895 3326729 0.024853805767934774 0.1679537187745822 chr13 115169878 1505195 0.013069346135801237 0.11943614319480417 chr14 107349540 2483982 0.023139195566185006 0.16301387875854262 chr15 102531392 1350468 0.01317126368478446 0.12181123803902841 chr16 90354753 1916055 0.021205912654091368 0.16311558830899864 chr17 81195210 1046846 0.012892952675410286 0.13123418100331122 chr18 78077248 2151175 0.027551880414637565 0.2922958260823788 chr19 59128983 1445444 0.02444560901715492 0.21753845559618978 chr20 63025520 1705961 0.02706778143202944 0.1762086885417352 chr21 48129895 984827 0.020461856399229626 0.15806625139958322 chr22 51304566 516190 0.010061287722422211 0.10461837159090642 chrMT 16571 5535 0.3340172590670448 0.5841159036588972 chrX 155270560 2792744 0.01798630725618559 0.1495322377695696 chrY 59373566 169724 0.0028585785128688412 0.07002248462356674