Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A7 F184 I0 R1 35 35.7 768239 98.7% 758251 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,289,262 C→G 100% W76C (TGG→TGC)  cdaA ← Cyclic di‑AMP synthase CdaA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,289,2620CG97.1% 65.9 / ‑5.6 29W76C (TGG→TGC) cdaACyclic di‑AMP synthase CdaA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base G (8/20);  minor base T (1/0);  total (9/20)
Fisher's exact test for biased strand distribution p-value = 3.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGA  >  USA300TCH1516_ALE/2289131‑2289397
                                                                                                                                   |                                                                                                                                       
gATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTAAGTCGACCAAGGTGTTCTAAGGCACGTCTAAATTCTGGTAGAAATATTCCTACCAAAGCTACTACCCCGCATTGAAt                                                                                                                                 <  1:160049/140‑1 (MQ=255)
                          aCTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTg                                                                                                       >  1:511207/1‑140 (MQ=255)
                                   aTTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTATCGCACGTCTAATTTCTGGTTGGAATATTACTATTATAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGt                                                                                              <  1:52414/140‑1 (MQ=255)
                                   aTTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGt                                                                                              <  1:65071/140‑1 (MQ=255)
                                     tAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACTCACGTCTAATTTCTGGTTGGAATATTACTTTTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTc                                                                                            <  1:444774/140‑1 (MQ=255)
                                             taGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCAt                                                                                    >  1:9647/1‑140 (MQ=255)
                                               gCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAACTTTTTCCCCTCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATAc                                                                                  >  1:752776/1‑140 (MQ=255)
                                                 gTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGGTCAATATCATACtt                                                                                >  1:314626/1‑140 (MQ=255)
                                                     tAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATct                                                                            <  1:298752/140‑1 (MQ=255)
                                                     tAAAAAGCTACCTCTACCAAGTTGTTATAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGGTGCAGTCAAGTTCAATATCATACTTATct                                                                            <  1:353282/140‑1 (MQ=255)
                                                        aaaGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATctgct                                                                         <  1:633565/140‑1 (MQ=255)
                                                        aaaGCTACCTCTACCAAGTTGGTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTAGTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATctgct                                                                         <  1:174709/140‑1 (MQ=255)
                                                               ccTCTACCAAGTTTTTCTAACGTACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAAt                                                                  <  1:512675/140‑1 (MQ=255)
                                                               ccTCTACCAAGTTGTTCTAACGCACGTTTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAAt                                                                  <  1:288518/140‑1 (MQ=255)
                                                               ccTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAAt                                                                  <  1:424988/140‑1 (MQ=255)
                                                                        aGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAAATGTTTCAGTCAACTTCAATATCTTACTAATGTGCTTACCAATAACAATTAc                                                         >  1:289003/1‑140 (MQ=255)
                                                                         gttgttCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACt                                                        <  1:634845/140‑1 (MQ=255)
                                                                         gttgttCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACt                                                        <  1:586834/140‑1 (MQ=255)
                                                                          ttgttCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTATATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACCATTACTa                                                       <  1:684597/140‑1 (MQ=255)
                                                                          ttgttCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTa                                                       <  1:503165/140‑1 (MQ=255)
                                                                             ttCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTACTGACCAATAACAATTACTAata                                                    >  1:38126/1‑140 (MQ=255)
                                                                               cTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAataac                                                  >  1:455940/1‑138 (MQ=255)
                                                                                   cGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACAAAATCAAATAATTTAGATGTAGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCACtt                                              >  1:202281/1‑140 (MQ=255)
                                                                                                 cTGGTTGGAATATTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATTTGCTGACCAATAACAATTACTAATATCCCTTTAATTAATTGTATc                                >  1:437030/1‑140 (MQ=255)
                                                                                                           tatTACTATTAATGCTCATACCCCGCTTTGAATAACGATATCGAATATTTTAGATGTTGCAGTCTAGTTCTATTTCATTCTTTTCTGCTGATCAATATCTATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTc                      <  1:27405/140‑1 (MQ=255)
                                                                                                            atTACTATTAAAGCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTcc                     <  1:400958/140‑1 (MQ=255)
                                                                                                                        gCTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGt         <  1:385531/140‑1 (MQ=255)
                                                                                                                         cTAATACCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGtg        <  1:352571/140‑1 (MQ=255)
                                                                                                                              aCCCCGCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATgag   <  1:264757/140‑1 (MQ=255)
                                                                                                                               ccccgcATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATgaga  <  1:539954/140‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                       
GATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGA  >  USA300TCH1516_ALE/2289131‑2289397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A