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
A2 F17 I0 R2 278 43.2 2215644 94.6% 2095999 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,132,803 G→A 28.8% intergenic (+119/‑38) arpB → / → yniD ECK1718:JW5278+JW1710:b4494; hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,132,8030GA28.8% 81.0 / 37.9 52intergenic (+119/‑38)arpB/yniDECK1718:JW5278+JW1710:b4494; hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (21/16);  new base A (7/8);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 5.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.66e-01

ACAGTGACCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTGGTATGCCGACTA  >  minE/1132742‑1132865
                                                             |                                                              
aCAGTGACCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTg                                                       >  1:107206/1‑71 (MQ=255)
 cAGTGACCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTATCCCTTTTGt                                                      <  1:1751586/71‑1 (MQ=255)
    tGACCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTa                                                    >  1:171196/1‑70 (MQ=255)
    tGACCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTa                                                    >  1:1499448/1‑70 (MQ=255)
          tgtgCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCg                                             >  1:731129/1‑71 (MQ=255)
            tgCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGt                                            >  1:340910/1‑70 (MQ=255)
             gCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGtt                                           <  1:1748348/70‑1 (MQ=255)
                     ccccccGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGca                                   >  1:1632762/4‑70 (MQ=255)
                     ccACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGca                                   >  1:1727042/1‑70 (MQ=255)
                     ccACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGca                                   >  1:1134744/1‑70 (MQ=255)
                        cccGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAag                               <  1:1725784/71‑1 (MQ=255)
                         ccGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTa                                                    <  1:1219747/49‑1 (MQ=255)
                         ccGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAaga                              <  1:1986956/71‑1 (MQ=255)
                         ccGACGGCTGTAATAACAAAAAATCCCTTGATGCCTATCCCTTTTGTTa                                                    <  1:369064/49‑1 (MQ=255)
                         ccGACGGCTGTAATAACAAAAAATCCCTTGATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAaga                              <  1:1537868/71‑1 (MQ=255)
                          cGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTaca                                                  >  1:1463218/1‑50 (MQ=255)
                          cGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAagag                             <  1:1960431/71‑1 (MQ=255)
                           gACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACaa                                >  1:2115366/1‑67 (MQ=255)
                            aCGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGtt                                           <  1:133238/55‑1 (MQ=255)
                            aCGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGtt                                           <  1:1711833/55‑1 (MQ=255)
                            aCGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAgaga                            <  1:1353999/70‑1 (MQ=255)
                              ggCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGatat                         <  1:1442994/71‑1 (MQ=255)
                                 tGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAcgag                             <  1:1360201/64‑1 (MQ=255)
                                  gTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAgaga                            <  1:1643780/64‑1 (MQ=255)
                                   taataaCAAAAAATCCCTTGATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAg                     >  1:1758994/1‑70 (MQ=255)
                                    aataaCAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGt                                            <  1:1578390/46‑1 (MQ=255)
                                    aataaCAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGt                                            <  1:1401876/46‑1 (MQ=255)
                                    aataaCAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGata                          >  1:1322874/1‑64 (MQ=255)
                                    aataaCAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGata                          >  1:911587/1‑64 (MQ=255)
                                     ataaCAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGata                          >  1:1776175/1‑63 (MQ=255)
                                     ataaCAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGa                   >  1:2080407/1‑70 (MQ=255)
                                     ataaCAAAAAATCCCTTGATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGa                   <  1:81151/70‑1 (MQ=255)
                                     ataaCAAAAAATCCCTTGATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGa                   <  1:955724/70‑1 (MQ=255)
                                      taaCAAAAAATCCCTTGATGCCTGTCCCCTTTGTTACACTCCGTTAt                                         <  1:1990231/47‑1 (MQ=255)
                                      taaCAAAAAATCCCTTGATGCCTATCCCTTTTGTTACACTCCGTTATCACGcac                                  <  1:975142/54‑1 (MQ=255)
                                       aaCAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGacac                >  1:2125819/1‑71 (MQ=255)
                                       aaCAAAAAATCCCTTGATGCCTATCCCTTTTGTTACACTCCGt                                            >  1:255704/1‑43 (MQ=255)
                                         cAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTg              >  1:782457/1‑71 (MQ=255)
                                           aaaaaTCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTgg             >  1:1224715/1‑70 (MQ=255)
                                           aaaaaTCCCTTGATGCCTATCCCTTTTGTTACACTCCGTTATCa                                       >  1:1244252/1‑44 (MQ=255)
                                            aaaaTCCCTTGATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTGGt            >  1:1843340/1‑70 (MQ=255)
                                               aTCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGcaca                                 <  1:164466/46‑1 (MQ=255)
                                               aTCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTGGTATGc        >  1:521450/1‑71 (MQ=255)
                                                 cccTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTGGTATGcc       >  1:700632/1‑70 (MQ=255)
                                                  ccTTGATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGGGATATGCAGGACACTGGTATGCCg      <  1:10626/70‑1 (MQ=255)
                                                      gATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGc                       >  1:1338977/1‑49 (MQ=255)
                                                      gATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGc                       >  1:1734934/1‑49 (MQ=255)
                                                      gATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGc                       >  1:2009277/1‑49 (MQ=255)
                                                      gATGCCTATCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTGGTATGCCGACTa  <  1:728519/70‑1 (MQ=255)
                                                        tGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTGGTATGcc       <  1:1519943/63‑1 (MQ=255)
                                                            tGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGacac                >  1:1621914/1‑50 (MQ=255)
                                                            tGTCCCTTTTGTTACACTCAGTTATCACGCACAagag                             >  1:203204/1‑37 (MQ=255)
                                                             |                                                              
ACAGTGACCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACACTCCGTTATCACGCACAAGAGATATGCAGGACACTGGTATGCCGACTA  >  minE/1132742‑1132865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A